From 9109c44f82afdaf08005d9aac322d09c4f88a75e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Fri, 20 Dec 2024 19:18:55 +0100 Subject: [PATCH 1/5] Extrac wfs from dev.workflowhub --- sources/bin/extract_galaxy_workflows.py | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index 9b464bfc..f7a65241 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -56,9 +56,9 @@ def init_by_importing(self, wf: dict) -> None: def init_from_search(self, wf: dict, source: str, tools: dict) -> None: self.source = source - if self.source == "WorkflowHub": + if "WorkflowHub" in self.source: self.id = wf["data"]["id"] - self.link = f"https://workflowhub.eu{ wf['data']['links']['self'] }" + self.link = f"https://{ source.lower() }.eu{ wf['data']['links']['self'] }" self.name = wf["data"]["attributes"]["title"] self.tags = [w.lower() for w in wf["data"]["attributes"]["tags"]] self.create_time = shared.format_date(wf["data"]["attributes"]["created_at"]) @@ -92,7 +92,7 @@ def add_creators(self, wf: dict) -> None: Get workflow creators """ self.creators = [] - if self.source == "WorkflowHub": + if "WorkflowHub" in self.source: creators = wf["data"]["attributes"]["creators"] if len(creators) == 0: other = wf["data"]["attributes"]["other_creators"] @@ -109,7 +109,7 @@ def add_tools(self, wf: dict) -> None: Extract list of tool ids from workflow """ tools = set() - if self.source == "WorkflowHub": + if "WorkflowHub" in self.source: for tool in wf["data"]["attributes"]["internals"]["steps"]: if tool["description"] is not None: tools.add(shared.shorten_tool_id(tool["description"])) @@ -123,10 +123,10 @@ def add_projects(self, wf: dict) -> None: """ Extract projects associated to workflow on WorkflowHub """ - if self.source == "WorkflowHub": + if "WorkflowHub" in self.source: for project in wf["data"]["relationships"]["projects"]["data"]: wfhub_project = shared.get_request_json( - f"https://workflowhub.eu/projects/{project['id']}", + f"https://{ self.source.lower() }.eu/projects/{project['id']}", {"Accept": "application/json"}, ) self.projects.append(wfhub_project["data"]["attributes"]["title"]) @@ -135,7 +135,7 @@ def test_tags(self, tags: dict) -> bool: """ Test if there are overlap between workflow tags and target tags """ - if self.source == "WorkflowHub": + if "WorkflowHub" in self.source: source = "workflowhub" else: source = "public" @@ -156,6 +156,7 @@ def __init__(self, test: bool = False) -> None: def init_by_searching(self, tool_fp: str) -> None: self.tools = shared.read_suite_per_tool_id(tool_fp) self.add_workflows_from_workflowhub() + self.add_workflows_from_workflowhub("dev.") self.add_workflows_from_public_servers() def init_by_importing(self, wfs: dict) -> None: @@ -164,13 +165,13 @@ def init_by_importing(self, wfs: dict) -> None: wf.init_by_importing(iwf) self.workflows.append(wf) - def add_workflows_from_workflowhub(self) -> None: + def add_workflows_from_workflowhub(self, prefix:str = "") -> None: """ Add workflows from WorkflowHub """ header = {"Accept": "application/json"} wfhub_wfs = shared.get_request_json( - "https://workflowhub.eu/workflows?filter[workflow_type]=galaxy", + f"https://{ prefix }workflowhub.eu/workflows?filter[workflow_type]=galaxy", header, ) print(f"Workflows from WorkflowHub: {len(wfhub_wfs['data'])}") @@ -179,12 +180,12 @@ def add_workflows_from_workflowhub(self) -> None: data = data[:10] for wf in data: wfhub_wf = shared.get_request_json( - f"https://workflowhub.eu{wf['links']['self']}", + f"https://{ prefix }workflowhub.eu{wf['links']['self']}", header, ) if wfhub_wf: wf = Workflow() - wf.init_from_search(wf=wfhub_wf, source="WorkflowHub", tools=self.tools) + wf.init_from_search(wf=wfhub_wf, source=f"{ prefix }WorkflowHub", tools=self.tools) self.workflows.append(wf) print(len(self.workflows)) From ea3e9c2d2277905ccfdc1ad2df2f1294c8804fa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sat, 21 Dec 2024 17:44:39 +0100 Subject: [PATCH 2/5] Add curation step --- sources/bin/extract_galaxy_workflows.py | 72 +++++++++++++++++++++++-- sources/bin/get_community_workflows.sh | 17 +++--- 2 files changed, 80 insertions(+), 9 deletions(-) diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index f7a65241..cdb544bc 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -5,6 +5,7 @@ Any, Dict, List, + Optional, ) import pandas as pd @@ -34,6 +35,8 @@ def __init__(self) -> None: self.license = "" self.doi = "" self.projects: List[str] = [] + self.keep = True + self.deprecated = False def init_by_importing(self, wf: dict) -> None: self.source = wf["source"] @@ -53,6 +56,8 @@ def init_by_importing(self, wf: dict) -> None: self.license = wf["license"] self.doi = wf["doi"] self.projects = wf["projects"] + self.keep = wf["keep"] + self.deprecated = wf["deprecated"] def init_from_search(self, wf: dict, source: str, tools: dict) -> None: self.source = source @@ -250,7 +255,17 @@ def filter_workflows_by_tags(self, tags: dict) -> None: to_keep_wf.append(w) self.workflows = to_keep_wf - def export_workflows_to_tsv(self, output_fp: str) -> None: + def curate_workflows(self, wf_status: Dict) -> None: + """ + Curate workflows based on community feedback + """ + curated_wfs = [] + for wf in self.workflows: + print(wf) + print(wf_status) + + + def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List[str]] = None) -> None: """ Export workflows to a TSV file """ @@ -272,6 +287,8 @@ def export_workflows_to_tsv(self, output_fp: str) -> None: "license": "License", "doi": "DOI", "projects": "Projects", + "keep": "To keep", + "deprecated": "Deprecated" } df = pd.DataFrame(self.export_workflows_to_dict()) @@ -280,6 +297,10 @@ def export_workflows_to_tsv(self, output_fp: str) -> None: df[col] = shared.format_list_column(df[col]) df = df.rename(columns=renaming).fillna("").reindex(columns=list(renaming.values())) + + if to_keep_columns is not None: + df = df[to_keep_columns] + df.to_csv(output_fp, sep="\t", index=False) @@ -316,13 +337,44 @@ def export_workflows_to_tsv(self, output_fp: str) -> None: "--filtered", "-f", required=True, - help="Filepath to TSV with filtered tutorials", + help="Filepath to JSON with filtered workflows", + ) + filterwf.add_argument( + "--tsv-filtered", + "-f", + required=True, + help="Filepath to TSV with filtered workflows", ) filterwf.add_argument( "--tags", "-c", help="Path to a YAML file with tags (different for public or WorkflowHub wfs) to keep in the extraction", ) + filterwf.add_argument( + "--status", + "-s", + help="Path to a TSV file with workflow status", + ) + + # Curate workflow + curatewf = subparser.add_parser("curate", help="Curate workflows based on community review") + curatewf.add_argument( + "--filtered", + "-f", + required=True, + help="Filepath to JSON with workflows filtered based on tags", + ) + curatewf.add_argument( + "--curated", + "-c", + required=True, + help="Filepath to TSV with curated workflows", + ) + curatewf.add_argument( + "--status", + "-s", + help="Path to a TSV file with workflow status", + ) args = parser.parse_args() @@ -336,4 +388,18 @@ def export_workflows_to_tsv(self, output_fp: str) -> None: wfs.init_by_importing(wfs=shared.load_json(args.all)) tags = shared.load_yaml(args.tags) wfs.filter_workflows_by_tags(tags) - wfs.export_workflows_to_tsv(args.filtered) + shared.export_to_json(wfs.export_workflows_to_dict(), args.filtered) + wfs.export_workflows_to_tsv(args.tsv_filtered) + wfs.export_workflows_to_tsv(args.status, to_keep_columns=["Name", "Link", "Source", "Projects", "To keep", "Deprecated"]) + + elif args.command == "curate": + wfs = Workflows() + wfs.init_by_importing(wfs=shared.load_json(args.filtered)) + try: + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + except Exception as ex: + print(f"Failed to load {args.status} file with:\n{ex}") + print("Not assigning tool status for this community !") + status = {} + wfs.curate_workflows(status) + wfs.export_workflows_to_tsv(args.curated) diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh index 2a7efde4..92b52430 100644 --- a/sources/bin/get_community_workflows.sh +++ b/sources/bin/get_community_workflows.sh @@ -24,13 +24,18 @@ else python sources/bin/extract_galaxy_workflows.py \ filter \ --all "communities/all/resources/workflows.json" \ - --filtered "communities/$community/resources/workflows.tsv" \ - --tags "communities/$community/metadata/workflow_tags" + --filtered "communities/$community/resources/tag_filtered_workflows.json" \ + --tsv-filtered "communities/$community/resources/tag_filtered_workflows.tsv" \ + --tags "communities/$community/metadata/workflow_tags" \ + --status "communities/$community/metadata/workflow_status.tsv" - python sources/bin/create_interactive_table.py \ - --input "communities/$community/resources/workflows.tsv" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/$community/resources/workflows.html" + if [[ -f "communities/$community/metadata/workflow_status.tsv" ]]; then + python sources/bin/extract_galaxy_workflows.py \ + curate \ + --filtered "communities/$community/resources/tag_filtered_workflows.json" \ + --status "communities/$community/metadata/workflow_status.tsv" \ + --curated "communities/$community/resources/curated_workflows.tsv" + fi; fi; fi; done From b642f9b6203cf96865b63e08054c2f6e698532d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sun, 22 Dec 2024 18:07:11 +0100 Subject: [PATCH 3/5] Add workflow_status file and curation step --- sources/README.md | 4 +- sources/bin/extract_galaxy_workflows.py | 67 +++++++++++++++++++------ sources/bin/get_community_tools.sh | 25 +++------ sources/bin/populate_labs.py | 5 +- 4 files changed, 64 insertions(+), 37 deletions(-) diff --git a/sources/README.md b/sources/README.md index 619abf08..1fd3fdfa 100644 --- a/sources/README.md +++ b/sources/README.md @@ -235,7 +235,7 @@ To make a test run of the tool to check its functionalities follow [Usage](#Usag This runs the tool, but only parses the test repository [Galaxy-Tool-Metadata-Extractor-Test-Wrapper](https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper) -2. Tool filter +2. Tool filter and curation ```bash $ bash sources/bin/get_community_tools.sh test @@ -269,7 +269,7 @@ To make a test run of the tool to check its functionalities follow [Usage](#Usag $ bash sources/bin/extract_all_workflows.sh test ``` -2. Workflow filtering +2. Workflow filtering and curation ```bash $ bash sources/bin/get_community_workflows.sh test diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index cdb544bc..9bb85ed9 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -56,8 +56,10 @@ def init_by_importing(self, wf: dict) -> None: self.license = wf["license"] self.doi = wf["doi"] self.projects = wf["projects"] - self.keep = wf["keep"] - self.deprecated = wf["deprecated"] + if "keep" in wf: + self.keep = wf["keep"] + if "deprecated" in wf: + self.deprecated = wf["deprecated"] def init_from_search(self, wf: dict, source: str, tools: dict) -> None: self.source = source @@ -147,6 +149,13 @@ def test_tags(self, tags: dict) -> bool: matches = set(self.tags) & set(tags[source]) return len(matches) != 0 + def update_status(self, wf: dict) -> None: + """ + Update status from status table + """ + self.keep = wf["To keep"] + self.deprecated = wf["Deprecated"] + class Workflows: """ @@ -170,7 +179,7 @@ def init_by_importing(self, wfs: dict) -> None: wf.init_by_importing(iwf) self.workflows.append(wf) - def add_workflows_from_workflowhub(self, prefix:str = "") -> None: + def add_workflows_from_workflowhub(self, prefix: str = "") -> None: """ Add workflows from WorkflowHub """ @@ -245,25 +254,28 @@ def export_workflows_to_dict(self) -> List: """ return [w.__dict__ for w in self.workflows] - def filter_workflows_by_tags(self, tags: dict) -> None: + def filter_workflows_by_tags(self, tags: dict, status: Dict) -> None: """ Filter workflows by tags """ to_keep_wf = [] for w in self.workflows: + if w.link in status: + w.update_status(status[w.link]) if w.test_tags(tags): to_keep_wf.append(w) self.workflows = to_keep_wf - def curate_workflows(self, wf_status: Dict) -> None: + def curate_workflows(self, status: Dict) -> None: """ Curate workflows based on community feedback """ curated_wfs = [] - for wf in self.workflows: - print(wf) - print(wf_status) - + for w in self.workflows: + if w.link in status and status[w.link]["To keep"]: + w.update_status(status[w.link]) + curated_wfs.append(w) + self.workflows = curated_wfs def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List[str]] = None) -> None: """ @@ -288,7 +300,7 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List "doi": "DOI", "projects": "Projects", "keep": "To keep", - "deprecated": "Deprecated" + "deprecated": "Deprecated", } df = pd.DataFrame(self.export_workflows_to_dict()) @@ -296,12 +308,19 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List for col in ["tools", "edam_operation", "edam_topic", "creators", "tags", "projects"]: df[col] = shared.format_list_column(df[col]) - df = df.rename(columns=renaming).fillna("").reindex(columns=list(renaming.values())) + df = ( + df.sort_values(by=["source", "projects"]) + .rename(columns=renaming) + .fillna("") + .reindex(columns=list(renaming.values())) + ) if to_keep_columns is not None: df = df[to_keep_columns] - df.to_csv(output_fp, sep="\t", index=False) + df_iwc = df.query("Projects == 'Intergalactic Workflow Commission (IWC)'") + df_no_iwc = df.query("Projects != 'Intergalactic Workflow Commission (IWC)'") + pd.concat([df_iwc, df_no_iwc]).to_csv(output_fp, sep="\t", index=False) if __name__ == "__main__": @@ -341,7 +360,7 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List ) filterwf.add_argument( "--tsv-filtered", - "-f", + "-t", required=True, help="Filepath to TSV with filtered workflows", ) @@ -387,10 +406,28 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List wfs = Workflows() wfs.init_by_importing(wfs=shared.load_json(args.all)) tags = shared.load_yaml(args.tags) - wfs.filter_workflows_by_tags(tags) + # get status if file provided + if args.status: + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + else: + status = {} + wfs.filter_workflows_by_tags(tags, status) shared.export_to_json(wfs.export_workflows_to_dict(), args.filtered) wfs.export_workflows_to_tsv(args.tsv_filtered) - wfs.export_workflows_to_tsv(args.status, to_keep_columns=["Name", "Link", "Source", "Projects", "To keep", "Deprecated"]) + wfs.export_workflows_to_tsv( + args.status, + to_keep_columns=[ + "Link", + "Name", + "Source", + "Projects", + "Creators", + "Creation time", + "Update time", + "To keep", + "Deprecated", + ], + ) elif args.command == "curate": wfs = Workflows() diff --git a/sources/bin/get_community_tools.sh b/sources/bin/get_community_tools.sh index 4b2772c4..95f2894e 100755 --- a/sources/bin/get_community_tools.sh +++ b/sources/bin/get_community_tools.sh @@ -37,15 +37,15 @@ else echo "$community"; mkdir -p "communities/$community/resources" - if [[ -f "communities/$community/metadata/tool_status.tsv" ]]; then - python sources/bin/extract_galaxy_tools.py \ - filter \ - --all "communities/all/resources/tools.json" \ - --categories "communities/$community/metadata/categories" \ - --tsv-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ - --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" \ - --status "communities/$community/metadata/tool_status.tsv" + python sources/bin/extract_galaxy_tools.py \ + filter \ + --all "communities/all/resources/tools.json" \ + --categories "communities/$community/metadata/categories" \ + --tsv-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ + --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" \ + --status "communities/$community/metadata/tool_status.tsv" + if [[ -f "communities/$community/metadata/tool_status.tsv" ]]; then python sources/bin/extract_galaxy_tools.py \ curate \ --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" \ @@ -62,15 +62,6 @@ else --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/$community/resources/tools_wordcloud.png" fi; - - else - python sources/bin/extract_galaxy_tools.py \ - filter \ - --all "communities/all/resources/tools.json" \ - --categories "communities/$community/metadata/categories" \ - --tsv-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ - --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" - fi; fi; fi; diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py index 9b2f943b..f7c9c196 100644 --- a/sources/bin/populate_labs.py +++ b/sources/bin/populate_labs.py @@ -2,7 +2,6 @@ import argparse import os -from typing import List import pandas as pd from ruamel.yaml import YAML as yaml @@ -70,7 +69,7 @@ def main() -> None: { "id": "more_tools", "title": "More tools !", - "heading_md": f"Request a new tools or look at the complete list", + "heading_md": "Request a new tools or look at the complete list", "content": entries, } ) @@ -127,7 +126,7 @@ def main() -> None: for group_id, group in top_items_per_category.groupby("Category"): tool_entries = [] - for index, row in group.iterrows(): + for _, row in group.iterrows(): # Prepare the description with an HTML unordered list and links for each Galaxy tool ID description = f"{row['Description']}\n (Tool usage: {row[count_column]})" From fdc6ba7450aa9402c6b494095686fc9f540584cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sun, 22 Dec 2024 18:08:33 +0100 Subject: [PATCH 4/5] Update workflow files --- communities/all/resources/workflows.json | 94086 +++++++++------- .../microgalaxy/metadata/workflow_status.tsv | 150 + .../resources/curated_workflows.tsv | 83 + .../resources/tag_filtered_workflows.json | 6924 ++ .../resources/tag_filtered_workflows.tsv | 163 + .../microgalaxy/resources/workflows.html | 2523 - .../microgalaxy/resources/workflows.tsv | 136 - 7 files changed, 62029 insertions(+), 42036 deletions(-) create mode 100644 communities/microgalaxy/metadata/workflow_status.tsv create mode 100644 communities/microgalaxy/resources/curated_workflows.tsv create mode 100644 communities/microgalaxy/resources/tag_filtered_workflows.json create mode 100644 communities/microgalaxy/resources/tag_filtered_workflows.tsv delete mode 100644 communities/microgalaxy/resources/workflows.html delete mode 100644 communities/microgalaxy/resources/workflows.tsv diff --git a/communities/all/resources/workflows.json b/communities/all/resources/workflows.json index 298d3679..2d001a07 100644 --- a/communities/all/resources/workflows.json +++ b/communities/all/resources/workflows.json @@ -1,4 +1,64 @@ [ + { + "create_time": "2024-12-17", + "creators": [ + "Galaxy", + " VGP" + ], + "doi": null, + "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Phasing", + "Transcriptome assembly", + "k-mer counting", + "Read pre-processing", + "De-novo assembly", + "Sequence trimming", + "Sequence assembly validation", + "Validation", + "Data handling" + ], + "edam_topic": [], + "id": "642", + "latest_version": 11, + "license": "CC-BY-4.0", + "link": "https://workflowhub.eu/workflows/642?version=11", + "name": "Assembly-Hifi-Trio-phasing-VGP5/main", + "number_of_steps": 40, + "projects": [ + "Intergalactic Workflow Commission (IWC)" + ], + "source": "WorkflowHub", + "tags": [], + "tools": [ + "", + "__EXTRACT_DATASET__", + "tp_find_and_replace", + "join1", + "tp_grep_tool", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", + "Convert characters1", + "busco", + "cutadapt", + "hifiasm", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", + "Cut1", + "tp_awk_tool" + ], + "update_time": "2024-12-17", + "versions": 11 + }, { "create_time": "2024-12-12", "creators": [ @@ -22,11 +82,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "meryl_count_kmers", - "pick_value", + "meryl_histogram_kmers", "meryl_groups_kmers", + "meryl_count_kmers", "genomescope", - "meryl_histogram_kmers" + "pick_value" ], "update_time": "2024-12-12", "versions": 8 @@ -54,12 +114,12 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "meryl_histogram_kmers", + "meryl_groups_kmers", "meryl_count_kmers", "meryl", - "pick_value", - "meryl_groups_kmers", "genomescope", - "meryl_histogram_kmers" + "pick_value" ], "update_time": "2024-12-12", "versions": 5 @@ -71,16 +131,16 @@ ], "doi": null, "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "1225", @@ -96,22 +156,22 @@ "tags": [], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2024-12-10", "versions": 1 @@ -124,10 +184,10 @@ ], "doi": "10.48546/workflowhub.workflow.1199.2", "edam_operation": [ - "Aggregation", "Visualisation", "Statistical calculation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [ "Metagenomics", @@ -151,23 +211,23 @@ ], "tools": [ "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", - "kraken2", - "krakentools_beta_diversity", "collection_element_identifiers", - "regex1", "add_line_to_file", - "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", - "Prepare alpha diversity summary file\nPaste1", - "est_abundance", + "kraken2", + "regex1", + "krakentools_kreport2krona", "cat_multiple", - "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1", "taxonomy_krona_chart", + "Prepare alpha diversity summary file\nPaste1", "collection_column_join", - "krakentools_alpha_diversity", - "__RELABEL_FROM_FILE__", + "krakentools_combine_kreports", + "est_abundance", + "krakentools_beta_diversity", + "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1", "Extract column name and fraction_total_reads from Bracken report\nCut1", - "krakentools_kreport2krona", - "krakentools_combine_kreports" + "__RELABEL_FROM_FILE__", + "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", + "krakentools_alpha_diversity" ], "update_time": "2024-12-10", "versions": 2 @@ -179,23 +239,23 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "Scaffolding", "Sequence contamination filtering", - "Data retrieval", + "Mapping", "Genome assembly", - "Sequence trimming", - "Genotyping", - "Sequence database search", "Sequence alignment", + "Phasing", + "Scaffolding", + "Sequencing quality control", + "Genotyping", + "Transcriptome assembly", "k-mer counting", + "De-novo assembly", + "Sequence alignment analysis", + "Sequence database search", + "Data retrieval", + "Sequence trimming", "Sequence assembly validation", - "Mapping", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Genomics" @@ -216,39 +276,39 @@ "qc" ], "tools": [ - "fastp", + "smudgeplot", + "sambamba_flagstat", + "__EXTRACT_DATASET__", + "pairtools_dedup", + "collapse_dataset", + "cooler_cload_tabix", + "lftp", + "sam_merge2", "bg_diamond", - "sambamba_merge", - "rseqc_bam_stat", "bedtools_makewindowsbed", + "cooler_csort_tabix", + "rseqc_bam_stat", + "bwa_mem2", "CONVERTER_fasta_to_fai", "blobtoolkit", - "pairtools_sort", + "fasterq_dump", "gfastats", - "sam_merge2", - "__EXTRACT_DATASET__", - "meryl", - "hicexplorer_hicplotmatrix", - "pairtools_dedup", + "busco", + "__FLATTEN__", + "genomescope", "pick_value", - "tp_text_file_with_recurring_lines", - "pairtools_split", + "merqury", "hicexplorer_hicmergematrixbins", + "meryl", "pairtools_parse", - "collapse_dataset", - "sambamba_flagstat", - "cooler_cload_tabix", - "busco", - "__FLATTEN__", + "pairtools_split", + "pairtools_sort", + "sambamba_merge", + "hicexplorer_hicplotmatrix", + "fastp", "datasets_download_genome", - "cooler_csort_tabix", - "Cut1", - "lftp", - "fasterq_dump", - "bwa_mem2", - "genomescope", - "smudgeplot", - "merqury" + "tp_text_file_with_recurring_lines", + "Cut1" ], "update_time": "2024-12-05", "versions": 3 @@ -260,26 +320,26 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "De-novo assembly", - "Sequencing quality control", - "Pairwise sequence alignment", - "Phasing", - "Scaffolding", "Sequence contamination filtering", - "Data retrieval", - "Genome assembly", - "Sequence trimming", - "Read pre-processing", - "Genotyping", - "Sequence database search", "Sequence alignment", + "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Transcriptome assembly", "k-mer counting", + "Sequence database search", + "Sequence trimming", "Sequence assembly validation", - "Primer removal", "Mapping", - "Transcriptome assembly" + "Genome assembly", + "Phasing", + "Genotyping", + "Pairwise sequence alignment", + "Read pre-processing", + "De-novo assembly", + "Sequence alignment analysis", + "Data retrieval", + "Data handling" ], "edam_topic": [ "Genomics" @@ -300,41 +360,41 @@ "qc" ], "tools": [ - "minimap2", - "fastp", + "smudgeplot", + "sambamba_flagstat", + "__EXTRACT_DATASET__", + "pairtools_dedup", + "collapse_dataset", + "cooler_cload_tabix", + "lftp", + "sam_merge2", "bg_diamond", - "sambamba_merge", - "rseqc_bam_stat", "bedtools_makewindowsbed", + "cooler_csort_tabix", + "rseqc_bam_stat", + "bwa_mem2", "CONVERTER_fasta_to_fai", "blobtoolkit", - "pairtools_sort", + "fasterq_dump", "gfastats", - "sam_merge2", - "__EXTRACT_DATASET__", - "meryl", - "hicexplorer_hicplotmatrix", - "pairtools_dedup", - "pick_value", - "tp_text_file_with_recurring_lines", - "pairtools_split", - "hicexplorer_hicmergematrixbins", - "pairtools_parse", - "collapse_dataset", - "sambamba_flagstat", - "cooler_cload_tabix", "busco", "__FLATTEN__", - "datasets_download_genome", - "cooler_csort_tabix", - "Cut1", - "lftp", - "fasterq_dump", - "bwa_mem2", "genomescope", - "smudgeplot", "cutadapt", - "merqury" + "pick_value", + "merqury", + "hicexplorer_hicmergematrixbins", + "meryl", + "pairtools_parse", + "pairtools_split", + "minimap2", + "pairtools_sort", + "sambamba_merge", + "hicexplorer_hicplotmatrix", + "fastp", + "datasets_download_genome", + "tp_text_file_with_recurring_lines", + "Cut1" ], "update_time": "2024-12-05", "versions": 2 @@ -347,20 +407,20 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "612", @@ -376,88 +436,28 @@ "tags": [], "tools": [ "", - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", - "Convert characters1", - "busco", - "hifiasm", - "tp_awk_tool", - "Cut1", + "Add_a_column1", "multiqc", - "cutadapt", - "merqury" - ], - "update_time": "2024-12-06", - "versions": 12 - }, - { - "create_time": "2024-12-04", - "creators": [ - "Galaxy", - " VGP" - ], - "doi": null, - "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "Sequence assembly visualisation", - "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", - "Read pre-processing", - "Genome assembly", - "Sequence trimming", - "Validation", - "Transcriptome assembly" - ], - "edam_topic": [], - "id": "642", - "latest_version": 10, - "license": "CC-BY-4.0", - "link": "https://workflowhub.eu/workflows/642?version=10", - "name": "Assembly-Hifi-Trio-phasing-VGP5/main", - "number_of_steps": 40, - "projects": [ - "Intergalactic Workflow Commission (IWC)" - ], - "source": "WorkflowHub", - "tags": [], - "tools": [ - "", - "bandage_image", - "tp_grep_tool", "gfastats", - "__EXTRACT_DATASET__", - "tp_cut_tool", - "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", - "join1", - "param_value_from_file", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-06", - "versions": 10 + "versions": 12 }, { "create_time": "2024-12-04", @@ -469,14 +469,14 @@ ], "doi": null, "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "403", @@ -499,23 +499,23 @@ "hifiasm" ], "tools": [ + "Paste1", "cat1", + "filter_tabular", "Add_a_column1", + "fastq_to_fasta_python", "datamash_transpose", - "tp_replace_in_column", - "meryl", + "fasta-stats", + "merqury", "Cut1", - "add_line_to_file", - "quast", - "tp_grep_tool", + "meryl", "tp_sed_tool", - "fasta-stats", "Convert characters1", + "quast", "busco", - "filter_tabular", - "fastq_to_fasta_python", - "Paste1", - "merqury" + "tp_replace_in_column", + "tp_grep_tool", + "add_line_to_file" ], "update_time": "2024-12-04", "versions": 7 @@ -543,8 +543,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2024-12-06", @@ -570,17 +570,17 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2024-12-06", "versions": 1 @@ -592,10 +592,10 @@ ], "doi": null, "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -676,15 +676,15 @@ ], "tools": [ "regexColumn1", - "tp_cut_tool", - "ecoregion_cluster_estimate", "unzip", - "Interactive tool jupyter notebook\ninteractive_tool_jupyter_notebook", - "ecoregion_taxa_seeker", - "mergeCols1", "filter_tabular", + "ecoregion_cluster_estimate", + "ecoregion_taxa_seeker", "ecoregion_brt_analysis", - "ecoregion_GeoNearestNeighbor" + "ecoregion_GeoNearestNeighbor", + "Interactive tool jupyter notebook\ninteractive_tool_jupyter_notebook", + "tp_cut_tool", + "mergeCols1" ], "update_time": "2024-12-09", "versions": 1 @@ -697,9 +697,9 @@ "doi": "10.48546/workflowhub.workflow.881.5", "edam_operation": [ "Sequence assembly validation", - "Transcriptome assembly", "Scaffolding", - "Genome assembly" + "Genome assembly", + "Transcriptome assembly" ], "edam_topic": [], "id": "881", @@ -717,11 +717,11 @@ "tsi-annotation" ], "tools": [ - "fgenesh_get_proteins", + "fgenesh_annotate", "jcvi_gff_stats", + "fgenesh_get_proteins", "fgenesh_get_mrnas_gc", "fgenesh_split", - "fgenesh_annotate", "busco", "fgenesh_merge" ], @@ -752,16 +752,16 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", - "tp_awk_tool", "collection_element_identifiers", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "decoupler_pseudobulk", + "tp_awk_tool" ], "update_time": "2024-11-22", "versions": 2 @@ -773,8 +773,8 @@ ], "doi": null, "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1201", @@ -789,20 +789,20 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-19", "versions": 2 @@ -844,10 +844,10 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Antimicrobial resistance prediction", "Genome assembly", - "Parsing" + "Data handling", + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "1189", @@ -868,24 +868,24 @@ ], "tools": [ "", - "staramr_search", - "hamronize_tool", - "abricate", + "collapse_dataset", "tp_find_and_replace", + "abricate", + "Cut1", + "Grep1", + "__APPLY_RULES__", + "staramr_search", "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", "hamronize_summarize", - "tp_split_on_column", - "collapse_dataset", - "cat_multi_datasets", "addValue", - "__APPLY_RULES__", + "hamronize_tool", "cat1", - "Cut1", + "tp_split_on_column", + "cat_multi_datasets", + "tp_text_file_with_recurring_lines", + "datamash_ops", "cast", - "shovill", - "Grep1" + "shovill" ], "update_time": "2024-11-14", "versions": 2 @@ -897,14 +897,14 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "1190", @@ -919,19 +919,19 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "collapse_dataset", - "tp_awk_tool", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "fastp", + "multiqc", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-11-12", "versions": 1 @@ -960,10 +960,10 @@ "ocean" ], "tools": [ - "Create a climatology interactively with notebooks", "Interactively subset you data.", - "Create a climatology (not interactively)", - "Final step to visualize in different way a ocean variable like the phosphate." + "Create a climatology interactively with notebooks", + "Final step to visualize in different way a ocean variable like the phosphate.", + "Create a climatology (not interactively)" ], "update_time": "2024-10-18", "versions": 1 @@ -1023,15 +1023,15 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", + "ncbi_blastn_wrapper", + "tp_cat", "gfastats", - "Cut1", "tp_sed_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-10-13", "versions": 8 @@ -1044,13 +1044,13 @@ ], "doi": null, "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -1066,22 +1066,22 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "bwa_mem2", "", - "bellerophon", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "compose_text_param", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-10-07", "versions": 12 @@ -1093,14 +1093,14 @@ ], "doi": null, "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "1177", @@ -1115,13 +1115,13 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "extract peptides\nCut1", - "Quantified-Proteins\nGrouping1", + "Quantified-Peptides\nGrouping1", "extracting microbial Proteins\nGrep1", "extract proteins\nCut1", "extracting microbial Peptides\nGrep1", - "Quantified-Peptides\nGrouping1", - "maxquant" + "Quantified-Proteins\nGrouping1", + "maxquant", + "extract peptides\nCut1" ], "update_time": "2024-10-07", "versions": 1 @@ -1133,18 +1133,18 @@ ], "doi": null, "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "155", @@ -1159,21 +1159,21 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2024-10-07", "versions": 5 @@ -1198,20 +1198,20 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-10-07", "versions": 9 @@ -1223,14 +1223,14 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "110", @@ -1250,26 +1250,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", + "\n __FLATTEN__", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "\n __FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", - "\n __FLATTEN__", + "ivar_trim", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "\n __FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-10-07", "versions": 10 @@ -1283,12 +1283,12 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "1043", @@ -1311,13 +1311,13 @@ "quality" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-11-26", "versions": 7 @@ -1331,14 +1331,14 @@ ], "doi": null, "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "1052", @@ -1362,12 +1362,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-11-23", "versions": 8 @@ -1379,15 +1379,15 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", + "Genome assembly", "Sequence alignment", + "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -1409,16 +1409,16 @@ "qc" ], "tools": [ - "bellerophon", - "pretext_map", - "gfa_to_fa", + "bwa_mem2", "param_value_from_file", - "yahs", "merqury", - "busco", - "bwa_mem2", + "yahs", + "gfa_to_fa", + "gfastats", "pretext_snapshot", - "gfastats" + "busco", + "pretext_map", + "bellerophon" ], "update_time": "2024-09-24", "versions": 1 @@ -1430,16 +1430,16 @@ ], "doi": "10.48546/workflowhub.workflow.1163.1", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -1462,13 +1462,13 @@ ], "tools": [ "cat1", - "gfa_to_fa", "param_value_from_file", - "minimap2", "merqury", - "purge_dups", + "gfastats", + "gfa_to_fa", "busco", - "gfastats" + "minimap2", + "purge_dups" ], "update_time": "2024-10-31", "versions": 1 @@ -1480,15 +1480,15 @@ ], "doi": "10.48546/workflowhub.workflow.1162.1", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly visualisation", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -1510,13 +1510,13 @@ "qc" ], "tools": [ - "gfa_to_fa", - "bandage_image", "param_value_from_file", "merqury", + "gfa_to_fa", + "gfastats", + "bandage_image", "busco", - "hifiasm", - "gfastats" + "hifiasm" ], "update_time": "2024-10-31", "versions": 1 @@ -1551,16 +1551,16 @@ "profiling" ], "tools": [ + "smudgeplot", + "param_value_from_file", "Add_a_column1", - "meryl", - "tp_cut_tool", - "Cut1", "tp_find_and_replace", - "param_value_from_file", - "tp_grep_tool", + "Cut1", + "meryl", "Convert characters1", + "tp_cut_tool", "genomescope", - "smudgeplot" + "tp_grep_tool" ], "update_time": "2024-09-18", "versions": 2 @@ -1572,16 +1572,16 @@ ], "doi": null, "edam_operation": [ - "Sequence conversion", - "DNA translation", - "Sequence composition calculation", - "DNA transcription", - "Sequencing quality control", "Statistical calculation", + "DNA translation", "Primer removal", - "Sequence trimming", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", - "Validation" + "Sequence trimming", + "DNA transcription", + "Validation", + "Sequence conversion" ], "edam_topic": [ "Whole genome sequencing" @@ -1602,8 +1602,8 @@ "hifi" ], "tools": [ - "collapse_dataset", "seqkit_stats", + "collapse_dataset", "multiqc", "fastqc", "cutadapt" @@ -1618,15 +1618,15 @@ ], "doi": null, "edam_operation": [ - "Sequence conversion", - "DNA translation", - "Sequence composition calculation", - "DNA transcription", - "Sequencing quality control", "Sequence contamination filtering", "Statistical calculation", + "DNA translation", + "Sequencing quality control", + "Sequence composition calculation", "Sequence trimming", - "Validation" + "DNA transcription", + "Validation", + "Sequence conversion" ], "edam_topic": [ "Whole genome sequencing" @@ -1647,12 +1647,12 @@ "illumina" ], "tools": [ - "collapse_dataset", "seqkit_stats", - "fastp", + "collapse_dataset", "multiqc", - "fastqc", - "__FLATTEN__" + "fastp", + "__FLATTEN__", + "fastqc" ], "update_time": "2024-09-18", "versions": 2 @@ -1662,18 +1662,18 @@ "creators": [], "doi": null, "edam_operation": [ - "Data handling", - "Antimicrobial resistance prediction", "Sequence contamination filtering", - "Genome assembly", + "Read binning", + "Sequence alignment", + "Parsing", + "Data handling", "Sequence trimming", "Genome alignment", - "Genome indexing", - "Parsing", "Read mapping", - "Sequence alignment", + "Genome assembly", "Multilocus sequence typing", - "Read binning", + "Genome indexing", + "Antimicrobial resistance prediction", "RNA-Seq analysis" ], "edam_topic": [], @@ -1692,17 +1692,17 @@ "antimicrobial resistance" ], "tools": [ - "hamronize_tool", - "srst2", - "sistr_cmd", "mob_recon", + "shovill", + "hamronize_summarize", "seqsero2", - "bbtools_bbduk", "kma_map", + "bbtools_tadpole", + "srst2", + "sistr_cmd", + "bbtools_bbduk", "__UNZIP_COLLECTION__", - "shovill", - "hamronize_summarize", - "bbtools_tadpole" + "hamronize_tool" ], "update_time": "2024-09-09", "versions": 1 @@ -1735,10 +1735,10 @@ "creators": [], "doi": null, "edam_operation": [ - "Data handling", - "Antimicrobial resistance prediction", "Genome assembly", - "Parsing" + "Data handling", + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "470", @@ -1759,13 +1759,13 @@ "antimicrobial resistance" ], "tools": [ - "hamronize_tool", - "abricate", + "shovill", "collapse_dataset", "tp_find_and_replace", - "shovill", + "abricate", "hamronize_summarize", - "staramr_search" + "staramr_search", + "hamronize_tool" ], "update_time": "2024-09-09", "versions": 1 @@ -1804,11 +1804,11 @@ "edam_operation": [ "De-novo assembly", "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", "Statistical calculation", "Genome assembly", + "Sequence assembly visualisation", "Mapping assembly", + "Sequencing quality control", "Cross-assembly" ], "edam_topic": [], @@ -1829,15 +1829,15 @@ "nanopore" ], "tools": [ - "porechop", - "collapse_dataset", "flye", - "bandage_image", + "bandage_info", "nanofilt", + "collapse_dataset", "fasta-stats", - "fastqc", + "porechop", "split_file_to_collection", - "bandage_info" + "bandage_image", + "fastqc" ], "update_time": "2024-09-03", "versions": 1 @@ -1897,10 +1897,10 @@ "ocean" ], "tools": [ - "Use of Sanntis", + "Remove useless * in the protein fasta file", "Create the protein fasta file", "Create TSV file for Sanntis", - "Remove useless * in the protein fasta file" + "Use of Sanntis" ], "update_time": "2024-08-21", "versions": 1 @@ -1912,12 +1912,12 @@ ], "doi": "10.48546/workflowhub.workflow.1096.1", "edam_operation": [ - "Sequence assembly validation", - "Data handling", - "Scaffolding", "Genome annotation", "Genome assembly", "Differential protein expression profiling", + "Sequence assembly validation", + "Scaffolding", + "Data handling", "Transcriptome assembly" ], "edam_topic": [ @@ -1941,11 +1941,11 @@ ], "tools": [ "collapse_dataset", - "omark", "lftp", + "agat", "busco", "tp_text_file_with_recurring_lines", - "agat" + "omark" ], "update_time": "2024-08-26", "versions": 1 @@ -1958,16 +1958,16 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "633", @@ -1982,22 +1982,22 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "cat1", "", + "cat1", + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "merqury", "gfastats", - "Cut1", - "tp_awk_tool", + "busco", "join1", - "param_value_from_file", "tp_cut_tool", - "tp_find_and_replace", "minimap2", - "merqury", - "compose_text_param", - "busco", - "purge_dups" + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-10-07", "versions": 13 @@ -2010,8 +2010,8 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "643", @@ -2027,12 +2027,12 @@ "tags": [], "tools": [ "", - "ggplot2_point", - "bionano_scaffold", - "Cut1", - "tp_find_and_replace", "param_value_from_file", - "gfastats" + "tp_find_and_replace", + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-10-13", "versions": 5 @@ -2045,16 +2045,16 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "751", @@ -2070,20 +2070,20 @@ "tags": [], "tools": [ "", + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-10-13", "versions": 7 @@ -2108,9 +2108,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Taxonomic analysis", "Rarefaction", - "Phylogenetic tree for diversity analysis" + "Phylogenetic tree for diversity analysis", + "Taxonomic analysis" ], "update_time": "2024-12-06", "versions": 2 @@ -2143,17 +2143,17 @@ "qcxms" ], "tools": [ - "qcxms_neutral_run", - "Remove failed runs\n__FILTER_FAILED_DATASETS__", - "ctb_im_conformers", - "tp_cut_tool", "param_value_from_file", - "qcxms_getres", + "ctb_im_conformers", "xtb_molecular_optimization", "qcxms_production_run", - "openbabel_compound_convert", + "tp_cat", "split_file_to_collection", - "tp_cat" + "qcxms_getres", + "openbabel_compound_convert", + "Remove failed runs\n__FILTER_FAILED_DATASETS__", + "tp_cut_tool", + "qcxms_neutral_run" ], "update_time": "2024-10-04", "versions": 2 @@ -2213,14 +2213,14 @@ "single-cell" ], "tools": [ - "snapatac2_plotting", + "collection_element_identifiers", "__EXTRACT_DATASET__", + "Show beginning1", + "snapatac2_plotting", "anndata_manipulate", - "collection_element_identifiers", - "__FILTER_FROM_FILE__", + "snapatac2_preprocessing", "snapatac2_clustering", - "Show beginning1", - "snapatac2_preprocessing" + "__FILTER_FROM_FILE__" ], "update_time": "2024-08-02", "versions": 1 @@ -2232,10 +2232,10 @@ ], "doi": null, "edam_operation": [ + "Differential gene expression analysis", "Dimensionality reduction", "Essential dynamics", - "Gene expression profiling", - "Differential gene expression analysis" + "Gene expression profiling" ], "edam_topic": [], "id": "1077", @@ -2253,18 +2253,18 @@ "scatac-seq" ], "tools": [ - "anndata_inspect", "snapatac2_plotting", - "anndata_ops", "scanpy_plot", - "anndata_manipulate", - "scanpy_inspect", - "scanpy_filter", + "anndata_ops", "Cut1", + "scanpy_inspect", "scanpy_normalize", + "anndata_manipulate", "snapatac2_preprocessing", + "snapatac2_clustering", "replace_column_with_key_value_file", - "snapatac2_clustering" + "scanpy_filter", + "anndata_inspect" ], "update_time": "2024-08-30", "versions": 1 @@ -2294,24 +2294,24 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-10-31", "versions": 3 @@ -2325,15 +2325,15 @@ ], "doi": "10.48546/workflowhub.workflow.1062.1", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "1062", @@ -2348,18 +2348,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-07-15", "versions": 1 @@ -2373,19 +2373,19 @@ ], "doi": "10.48546/workflowhub.workflow.1061.1", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "1061", @@ -2400,23 +2400,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-07-15", "versions": 1 @@ -2432,12 +2432,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "1060", @@ -2452,28 +2452,28 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-07-15", "versions": 1 @@ -2487,9 +2487,9 @@ ], "doi": "10.48546/workflowhub.workflow.1059.1", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "1059", @@ -2504,8 +2504,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-07-15", @@ -2518,8 +2518,8 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "1057", @@ -2534,18 +2534,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-06-28", "versions": 2 @@ -2557,13 +2557,13 @@ ], "doi": "10.48546/workflowhub.workflow.1054.1", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -2582,19 +2582,19 @@ "tsi" ], "tools": [ + "bwa_mem2", "", - "bellerophon", "__EXTRACT_DATASET__", - "ggplot2_point", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", + "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-06-21", "versions": 1 @@ -2626,8 +2626,8 @@ "tsi-annotation" ], "tools": [ - "repeatmasker_wrapper", - "repeatmodeler" + "repeatmodeler", + "repeatmasker_wrapper" ], "update_time": "2024-06-20", "versions": 3 @@ -2657,9 +2657,9 @@ "tags": [], "tools": [ "map_param_value", - "brew3r_r", "stringtie", - "stringtie_merge" + "stringtie_merge", + "brew3r_r" ], "update_time": "2024-10-10", "versions": 2 @@ -2673,16 +2673,16 @@ ], "doi": null, "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "1050", @@ -2704,12 +2704,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-26", "versions": 9 @@ -2724,8 +2724,8 @@ "doi": null, "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "1049", @@ -2751,10 +2751,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-27", "versions": 7 @@ -2766,19 +2766,19 @@ ], "doi": null, "edam_operation": [ - "Sequence alignment analysis", - "Global alignment", + "Sequence contamination filtering", + "Phylogenetic tree generation", + "Sequence alignment", "Sequencing quality control", "Local alignment", + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment", "Variant calling", - "Phylogenetic tree generation", - "Sequence alignment", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", - "Taxonomic classification", + "Validation", "Phylogenetic tree visualisation", - "Sequence analysis", - "Validation" + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [ "Genetic variation", @@ -2802,20 +2802,20 @@ "tuberculosis" ], "tools": [ - "tb_profiler_profile", - "tbvcfreport", + "bcftools_consensus", "kraken2", + "EMBOSS: seqret84", + "fastp", + "multiqc", "tp_awk_tool", - "bcftools_consensus", "tb_variant_filter", - "snippy", "tp_sed_tool", - "EMBOSS: seqret84", + "tbvcfreport", + "__FLATTEN__", + "snippy", "mosdepth", - "fastp", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__" + "tb_profiler_profile", + "qualimap_bamqc" ], "update_time": "2024-06-12", "versions": 1 @@ -2829,11 +2829,11 @@ ], "doi": "10.48546/workflowhub.workflow.888.2", "edam_operation": [ + "Standardisation and normalisation", "Filtering", - "Format validation", - "Spectral library search", "Annotation", - "Standardisation and normalisation" + "Format validation", + "Spectral library search" ], "edam_topic": [ "Compound libraries and screening", @@ -2857,20 +2857,20 @@ "metabolomics" ], "tools": [ - "matchms_add_key", + "recetox_msfinder", "matchms_convert", - "column_remove_by_header", - "tp_find_and_replace", "matchms_subsetting", + "matchms_metadata_export", + "tp_find_and_replace", + "column_remove_by_header", "matchms_remove_key", - "recetox_msfinder", + "use_theoretical_mz_annotations", + "msmetaenhancer", "matchms_filtering", - "matchms_metadata_export", "tabular_to_csv", "csv_to_tabular", - "use_theoretical_mz_annotations", - "msmetaenhancer", - "rem_complex" + "rem_complex", + "matchms_add_key" ], "update_time": "2024-06-19", "versions": 2 @@ -2882,10 +2882,10 @@ ], "doi": null, "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -2902,8 +2902,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-12-06", "versions": 3 @@ -2915,10 +2915,10 @@ ], "doi": null, "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -2998,12 +2998,12 @@ "scrnaseq" ], "tools": [ - "anndata_inspect", - "cellranger", - "anndata_manipulate", "scanpy_read_10x", + "anndata_manipulate", "tp_sed_tool", - "tp_text_file_with_recurring_lines" + "cellranger", + "tp_text_file_with_recurring_lines", + "anndata_inspect" ], "update_time": "2024-05-30", "versions": 2 @@ -3098,18 +3098,18 @@ "scrnaseq" ], "tools": [ - "anndata_inspect", + "scanpy_find_cluster", + "tp_head_tool", "scanpy_plot", "scanpy_compute_graph", - "scanpy_plot_embed", - "tp_head_tool", + "scanpy_run_umap", "scanpy_find_markers", + "scanpy_run_pca", + "anndata_inspect", "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_plot_embed", "scanpy_scale_data", - "scanpy_run_pca", - "scanpy_run_umap" + "scanpy_normalise_data" ], "update_time": "2024-05-30", "versions": 3 @@ -3143,10 +3143,10 @@ "scrnaseq" ], "tools": [ + "scanpy_filter_cells", "scanpy_plot", - "scanpy_multiplet_scrublet", "anndata_ops", - "scanpy_filter_cells" + "scanpy_multiplet_scrublet" ], "update_time": "2024-05-30", "versions": 4 @@ -3180,14 +3180,14 @@ "scrnaseq" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", - "collapse_dataset", "scanpy_read_10x", + "collapse_dataset", + "anndata_manipulate", "rna_starsolo", "tp_sed_tool", - "__UNZIP_COLLECTION__", - "tp_text_file_with_recurring_lines" + "tp_text_file_with_recurring_lines", + "anndata_inspect", + "__UNZIP_COLLECTION__" ], "update_time": "2024-05-30", "versions": 3 @@ -3219,11 +3219,11 @@ "scrnaseq" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", "scanpy_read_10x", + "anndata_manipulate", "tp_sed_tool", - "tp_text_file_with_recurring_lines" + "tp_text_file_with_recurring_lines", + "anndata_inspect" ], "update_time": "2024-05-30", "versions": 2 @@ -3236,8 +3236,8 @@ ], "doi": "10.48546/workflowhub.workflow.880.1", "edam_operation": [ - "Data handling", - "Sequence file editing" + "Sequence file editing", + "Data handling" ], "edam_topic": [], "id": "880", @@ -3255,18 +3255,18 @@ "tsi-annotation" ], "tools": [ + "Paste1", + "tab2fasta", + "seqtk_seq", + "Cut1", + "tp_replace_in_line", + "seqtk_subseq", "fasta2tab", "tp_sort_header_tool", - "seqtk_subseq", - "tp_awk_tool", - "Cut1", - "tab2fasta", - "tp_grep_tool", "tp_sed_tool", - "tp_replace_in_line", - "seqtk_seq", - "fasta_compute_length", - "Paste1" + "tp_grep_tool", + "tp_awk_tool", + "fasta_compute_length" ], "update_time": "2024-05-09", "versions": 1 @@ -3279,12 +3279,12 @@ ], "doi": "10.48546/workflowhub.workflow.879.1", "edam_operation": [ - "Sequence assembly validation", - "Scaffolding", + "Coding region prediction", "De-novo assembly", "Genome assembly", - "Coding region prediction", "de Novo sequencing", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -3303,9 +3303,9 @@ "tsi-annotation" ], "tools": [ - "transdecoder", + "tp_sed_tool", "busco", - "tp_sed_tool" + "transdecoder" ], "update_time": "2024-05-09", "versions": 1 @@ -3318,8 +3318,8 @@ ], "doi": "10.48546/workflowhub.workflow.878.1", "edam_operation": [ - "Mapping", "RNA-Seq analysis", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -3338,14 +3338,14 @@ "tsi-annotation" ], "tools": [ - "seq_filter_by_id", - "cpat", - "tp_cut_tool", "skipping 1 header line\nFilter1", "stringtie_merge", + "gtftobed12", "tp_sed_tool", + "tp_cut_tool", + "cpat", "bedtools_getfastabed", - "gtftobed12" + "seq_filter_by_id" ], "update_time": "2024-05-09", "versions": 1 @@ -3392,10 +3392,10 @@ ], "doi": "10.48546/workflowhub.workflow.876.1", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "876", @@ -3415,12 +3415,12 @@ "tools": [ "__EXTRACT_DATASET__", "trimmomatic", - "Cut1", - "Remove beginning1", "multiqc", - "fastqc", + "tp_cat", + "Remove beginning1", "tp_replace_in_column", - "tp_cat" + "fastqc", + "Cut1" ], "update_time": "2024-05-09", "versions": 1 @@ -3504,9 +3504,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "interpolation_run_idw_interpolation", "graphicsmagick_image_compare", "Filter1", - "interpolation_run_idw_interpolation", "tabular_to_csv" ], "update_time": "2024-03-28", @@ -3520,14 +3520,14 @@ ], "doi": null, "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "794", @@ -3550,23 +3550,23 @@ "hifiasm" ], "tools": [ + "Paste1", "cat1", + "filter_tabular", "Add_a_column1", + "fastq_to_fasta_python", "datamash_transpose", - "tp_replace_in_column", - "meryl", + "fasta-stats", + "merqury", "Cut1", - "add_line_to_file", - "quast", - "tp_grep_tool", + "meryl", "tp_sed_tool", - "fasta-stats", "Convert characters1", + "quast", "busco", - "filter_tabular", - "fastq_to_fasta_python", - "Paste1", - "merqury" + "tp_replace_in_column", + "tp_grep_tool", + "add_line_to_file" ], "update_time": "2024-08-06", "versions": 2 @@ -3578,8 +3578,8 @@ ], "doi": null, "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "790", @@ -3596,17 +3596,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-06-02", "versions": 2 @@ -3618,18 +3618,18 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", - "Phasing", + "Genome assembly", "Sequence alignment", "Sequence assembly visualisation", - "k-mer counting", - "Sequence assembly validation", + "Phasing", "Scaffolding", - "Genome assembly", "Optimisation and refinement", - "Transcriptome assembly" + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Pairwise sequence alignment", + "Sequence assembly validation", + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -3651,21 +3651,21 @@ "name:ont" ], "tools": [ + "bwa_mem2", + "param_value_from_file", "Add_a_column1", + "merqury", "sam_merge2", "gfa_to_fa", + "gfastats", "bandage_image", - "param_value_from_file", "hypo", - "datamash_ops", - "minimap2", - "merqury", + "tables_arithmetic_operations", "busco", - "bwa_mem2", - "nextdenovo", "__FLATTEN__", - "tables_arithmetic_operations", - "gfastats" + "nextdenovo", + "minimap2", + "datamash_ops" ], "update_time": "2024-03-11", "versions": 1 @@ -3677,20 +3677,20 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Transcriptome assembly", - "De-novo assembly", - "Pairwise sequence alignment", + "Genome assembly", "Sequence alignment", - "Phasing", "Sequence assembly visualisation", - "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Genome assembly", "Mapping assembly", + "Phasing", + "Scaffolding", "Optimisation and refinement", - "Cross-assembly" + "Cross-assembly", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Pairwise sequence alignment", + "Sequence assembly validation", + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -3712,17 +3712,17 @@ "name:ont" ], "tools": [ - "sam_merge2", + "bwa_mem2", + "param_value_from_file", "flye", + "merqury", + "sam_merge2", "gfastats", - "hypo", "bandage_image", - "param_value_from_file", - "minimap2", + "hypo", "busco", - "bwa_mem2", "__FLATTEN__", - "merqury" + "minimap2" ], "update_time": "2024-03-11", "versions": 1 @@ -3776,23 +3776,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "biobb_io_pdb_ext", + "biobb_amber_leap_gen_top_ext", + "biobb_structure_utils_extract_chain_ext", "biobb_amber_sander_mdrun_ext", + "biobb_model_fix_altlocs_ext", + "biobb_structure_utils_structure_check_ext", "biobb_io_canonical_fasta_ext", + "biobb_model_fix_amides_ext", + "biobb_model_fix_backbone_ext", "biobb_model_fix_chirality_ext", - "biobb_io_pdb_ext", - "biobb_structure_utils_structure_check_ext", - "biobb_model_fix_altlocs_ext", + "biobb_structure_utils_extract_model_ext", "biobb_model_fix_ssbonds_ext", + "biobb_structure_utils_remove_molecules_ext", "biobb_model_fix_side_chain_ext", - "biobb_structure_utils_extract_model_ext", - "biobb_model_fix_amides_ext", - "biobb_amber_amber_to_pdb_ext", "biobb_chemistry_reduce_remove_hydrogens_ext", - "biobb_amber_leap_gen_top_ext", - "biobb_structure_utils_extract_chain_ext", - "biobb_model_fix_backbone_ext", "biobb_structure_utils_remove_pdb_water_ext", - "biobb_structure_utils_remove_molecules_ext" + "biobb_amber_amber_to_pdb_ext" ], "update_time": "2024-03-05", "versions": 1 @@ -3804,10 +3804,10 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "771", @@ -3823,12 +3823,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-11-15", "versions": 2 @@ -3860,21 +3860,21 @@ "zika" ], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2024-03-02", "versions": 1 @@ -3909,21 +3909,21 @@ "rna virus" ], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2024-03-02", "versions": 1 @@ -3958,21 +3958,21 @@ "rna virus" ], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2024-03-02", "versions": 1 @@ -4005,21 +4005,21 @@ "zika" ], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2024-03-02", "versions": 1 @@ -4049,8 +4049,8 @@ "astronomy" ], "tools": [ - "grb-detection_astro_tool", "hess_astro_tool", + "grb-detection_astro_tool", "lightcurve_analysis_astro_tool_pr91" ], "update_time": "2024-03-01", @@ -4080,11 +4080,11 @@ "genome-annotation" ], "tools": [ - "create_or_update", "list_organism", "iframe", - "jbrowse", - "create_account" + "create_account", + "create_or_update", + "jbrowse" ], "update_time": "2024-02-15", "versions": 1 @@ -4140,8 +4140,8 @@ ], "tools": [ "tp_cut_tool", - "obisindicators", - "csv_to_tabular" + "csv_to_tabular", + "obisindicators" ], "update_time": "2024-02-15", "versions": 1 @@ -4166,8 +4166,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "pm_muairss_read", - "pm_uep_opt" + "pm_uep_opt", + "pm_muairss_read" ], "update_time": "2024-02-15", "versions": 1 @@ -4194,8 +4194,8 @@ "climate" ], "tools": [ - "interactive_tool_copernicus_notebook", - "interactive_tool_panoply" + "interactive_tool_panoply", + "interactive_tool_copernicus_notebook" ], "update_time": "2024-02-15", "versions": 1 @@ -4207,13 +4207,13 @@ ], "doi": null, "edam_operation": [ - "Protein feature detection", - "Fold recognition", "Genome annotation", - "Sequence motif recognition", "Homology-based gene prediction", - "Query and retrieval", - "Information extraction" + "Information extraction", + "Sequence motif recognition", + "Protein feature detection", + "Fold recognition", + "Query and retrieval" ], "edam_topic": [], "id": "755", @@ -4243,20 +4243,20 @@ ], "doi": null, "edam_operation": [ - "Protein feature detection", - "Sequence annotation", + "Genome annotation", + "Homology-based gene prediction", + "Information extraction", + "Sequence motif recognition", "Genome assembly", "Sequence alignment", "Fold recognition", - "Genome visualisation", - "Genome annotation", - "Sequence motif recognition", - "Homology-based gene prediction", + "Scaffolding", "Query and retrieval", + "Transcriptome assembly", + "Protein feature detection", "Sequence assembly validation", - "Scaffolding", - "Information extraction", - "Transcriptome assembly" + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "754", @@ -4273,15 +4273,15 @@ "genome-annotation" ], "tools": [ - "interproscan", - "funannotate_annotate", + "jbrowse", "aegean_parseval", - "rna_star", "eggnog_mapper", - "jbrowse", + "interproscan", "busco", + "rna_star", "funannotate_compare", - "funannotate_predict" + "funannotate_predict", + "funannotate_annotate" ], "update_time": "2024-02-15", "versions": 1 @@ -4293,9 +4293,9 @@ ], "doi": null, "edam_operation": [ - "RNA-Seq analysis", "Genome annotation", - "Editing" + "Editing", + "RNA-Seq analysis" ], "edam_topic": [], "id": "753", @@ -4312,8 +4312,8 @@ "genome-annotation" ], "tools": [ - "repeatmasker_wrapper", - "red" + "red", + "repeatmasker_wrapper" ], "update_time": "2024-02-15", "versions": 1 @@ -4325,13 +4325,13 @@ ], "doi": null, "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "750", @@ -4346,10 +4346,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-06-13", "versions": 2 @@ -4419,15 +4419,15 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", + "Genome assembly", "Sequence alignment", + "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -4448,16 +4448,16 @@ "name:assembly+qc" ], "tools": [ - "bellerophon", - "pretext_map", - "gfa_to_fa", + "bwa_mem2", "param_value_from_file", - "yahs", "merqury", - "busco", - "bwa_mem2", + "yahs", + "gfa_to_fa", + "gfastats", "pretext_snapshot", - "gfastats" + "busco", + "pretext_map", + "bellerophon" ], "update_time": "2024-01-09", "versions": 1 @@ -4469,16 +4469,16 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -4499,13 +4499,13 @@ "name:assembly+qc" ], "tools": [ - "gfa_to_fa", "param_value_from_file", - "minimap2", "merqury", - "purge_dups", + "gfastats", + "gfa_to_fa", "busco", - "gfastats" + "minimap2", + "purge_dups" ], "update_time": "2024-01-09", "versions": 1 @@ -4540,16 +4540,16 @@ "name:profiling" ], "tools": [ + "smudgeplot", + "param_value_from_file", "Add_a_column1", - "meryl", - "tp_cut_tool", - "Cut1", "tp_find_and_replace", - "param_value_from_file", - "tp_grep_tool", + "Cut1", + "meryl", "Convert characters1", + "tp_cut_tool", "genomescope", - "smudgeplot" + "tp_grep_tool" ], "update_time": "2024-01-08", "versions": 1 @@ -4561,11 +4561,11 @@ ], "doi": null, "edam_operation": [ - "Sequence conversion", + "Sequence trimming", "Scatter plot plotting", "DNA translation", - "Sequence trimming", "DNA transcription", + "Sequence conversion", "Box-Whisker plot plotting" ], "edam_topic": [ @@ -4587,9 +4587,9 @@ "ont" ], "tools": [ + "collapse_dataset", "seqkit_stats", - "nanoplot", - "collapse_dataset" + "nanoplot" ], "update_time": "2024-01-08", "versions": 1 @@ -4601,16 +4601,16 @@ ], "doi": "10.48546/workflowhub.workflow.606.2", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -4631,13 +4631,13 @@ "hifi" ], "tools": [ - "gfa_to_fa", "param_value_from_file", - "minimap2", "merqury", - "purge_dups", + "gfastats", + "gfa_to_fa", "busco", - "gfastats" + "minimap2", + "purge_dups" ], "update_time": "2024-03-13", "versions": 1 @@ -4671,9 +4671,9 @@ ], "tools": [ "", - "cite_seq_count", + "pick_value", "tp_awk_tool", - "pick_value" + "cite_seq_count" ], "update_time": "2024-10-07", "versions": 5 @@ -4686,9 +4686,9 @@ ], "doi": null, "edam_operation": [ - "RNA-Seq analysis", + "Annotation", "Gene functional annotation", - "Annotation" + "RNA-Seq analysis" ], "edam_topic": [], "id": "689", @@ -4710,13 +4710,13 @@ "limma_voom", "Add_a_column1", "__EXTRACT_DATASET__", + "tp_replace_in_line", "tp_sort_header_tool", - "Cut1", + "collection_column_join", "join1", "tp_sorted_uniq", - "tp_replace_in_line", "annotatemyids", - "collection_column_join", + "Cut1", "goseq" ], "update_time": "2024-01-24", @@ -4730,17 +4730,17 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "688", @@ -4759,13 +4759,13 @@ "covid-19" ], "tools": [ - "rseqc_read_distribution", + "rseqc_geneBody_coverage", "featurecounts", - "hisat2", + "cutadapt", "multiqc", - "rseqc_geneBody_coverage", "fastqc", - "cutadapt" + "hisat2", + "rseqc_read_distribution" ], "update_time": "2024-01-24", "versions": 1 @@ -4804,13 +4804,13 @@ ], "doi": null, "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "680", @@ -4832,13 +4832,13 @@ "workflow4metabolomics" ], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "checkFormat", "xcms_plot_chromatogram", - "Multivariate" + "msnbase_readmsdata", + "checkFormat", + "Multivariate", + "xcms_merge" ], "update_time": "2024-06-13", "versions": 1 @@ -4863,22 +4863,22 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "gmx_em", - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "d354bc62a13564f8" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "d354bc62a13564f8", + "md_converter", + "gmx_sim" ], "update_time": "2024-07-01", "versions": 4 @@ -4890,13 +4890,13 @@ ], "doi": null, "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "677", @@ -4918,15 +4918,15 @@ "xcms" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", - "xcms_plot_chromatogram", + "abims_xcms_xcmsSet", "abims_xcms_retcor", - "abims_xcms_group" + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport" ], "update_time": "2024-07-13", "versions": 1 @@ -4941,18 +4941,18 @@ ], "doi": "10.48546/workflowhub.workflow.676.1", "edam_operation": [ + "Copy number estimation", + "Statistical calculation", "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", "Sequence alignment", - "Statistical calculation", - "Copy number estimation", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [ "Copy number variation", @@ -4975,22 +4975,22 @@ "variant-analysis" ], "tools": [ - "bwa_mem", - "bamleftalign", "samtools_calmd", + "samtools_rmdup", "__EXTRACT_DATASET__", + "control_freec", "trimmomatic", - "circos", - "samtools_view", - "samtools_rmdup", - "tp_replace_in_line", + "fastqc", "multiqc", + "tp_replace_in_line", + "__BUILD_LIST__", + "Grep1", + "bwa_mem", "tp_text_file_with_recurring_lines", + "circos", + "bamleftalign", "__RELABEL_FROM_FILE__", - "fastqc", - "control_freec", - "__BUILD_LIST__", - "Grep1" + "samtools_view" ], "update_time": "2024-04-03", "versions": 1 @@ -5006,8 +5006,8 @@ "doi": "10.48546/workflowhub.workflow.624.1", "edam_operation": [ "Phylogenetic tree analysis", - "Nucleic acid sequence analysis", - "Visualisation" + "Visualisation", + "Nucleic acid sequence analysis" ], "edam_topic": [ "Metagenomic sequencing", @@ -5030,14 +5030,14 @@ ], "tools": [ "", - "metaphlan2krona", - "metaphlan2", - "Cut1", - "taxonomy_krona_chart", "humann2_renorm_table", - "humann2", + "taxonomy_krona_chart", "humann2_regroup_table", - "merge_metaphlan_tables" + "merge_metaphlan_tables", + "metaphlan2", + "metaphlan2krona", + "humann2", + "Cut1" ], "update_time": "2024-04-05", "versions": 1 @@ -5067,9 +5067,9 @@ "tags": [], "tools": [ "tp_cut_tool", - "obisindicators", "Filter1", - "csv_to_tabular" + "csv_to_tabular", + "obisindicators" ], "update_time": "2024-12-09", "versions": 1 @@ -5098,9 +5098,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "cb_dissim", "cb_ivr", - "cb_div", - "cb_dissim" + "cb_div" ], "update_time": "2024-12-09", "versions": 1 @@ -5130,11 +5130,11 @@ "tools": [ "cat1", "regex1", - "Remove beginning1", - "Grouping1", "tp_head_tool", + "tp_cat", "Grep1", - "tp_cat" + "Remove beginning1", + "Grouping1" ], "update_time": "2024-12-09", "versions": 1 @@ -5161,15 +5161,15 @@ "tags": [], "tools": [ "cat1", - "table_compute", - "keras_model_config", "sklearn_to_categorical", "sklearn_fitted_model_eval", - "ml_visualization_ex", "model_prediction", - "Remove beginning1", + "table_compute", "keras_train_and_eval", - "keras_model_builder" + "Remove beginning1", + "keras_model_config", + "keras_model_builder", + "ml_visualization_ex" ], "update_time": "2024-12-09", "versions": 1 @@ -5199,10 +5199,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "ecoregion_clara_cluster", + "ecoregion_eco_map", "ecoregion_cluster_estimate", "ecoregion_taxa_seeker", - "ecoregion_eco_map", - "ecoregion_clara_cluster", "ecoregion_brt_analysis" ], "update_time": "2024-12-09", @@ -5234,10 +5234,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "srs_diversity_maps", + "srs_spectral_indices", "srs_preprocess_s2", "srs_global_indices", - "srs_spectral_indices" + "srs_diversity_maps" ], "update_time": "2024-12-09", "versions": 1 @@ -5267,11 +5267,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "ecology_stat_presence_abs", "tool_anonymization", + "ecology_beta_diversity", "ecology_presence_abs_abund", "ecology_link_between_var", - "ecology_stat_presence_abs", - "ecology_beta_diversity", "ecology_homogeneity_normality" ], "update_time": "2024-12-09", @@ -5285,8 +5285,8 @@ ], "doi": "10.48546/workflowhub.workflow.655.1", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequence analysis", "Sequencing quality control" ], @@ -5309,22 +5309,22 @@ "tags": [], "tools": [ "seq_filter_by_id", + "unzip", "obi_illumina_pairend", - "fastq_groomer", "obi_annotate", + "obi_stat", + "obi_tab", "wc_gnu", - "obi_ngsfilter", + "Filter1", + "ncbi_blastn_wrapper", + "obi_uniq", + "obi_clean", + "fastqc", "join1", "Cut1", - "unzip", - "obi_tab", - "obi_stat", - "fastqc", - "ncbi_blastn_wrapper", - "Filter1", "obi_grep", - "obi_clean", - "obi_uniq" + "obi_ngsfilter", + "fastq_groomer" ], "update_time": "2024-12-09", "versions": 1 @@ -5339,16 +5339,16 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "653", @@ -5365,9 +5365,9 @@ "metagenomics" ], "tools": [ - "mothur_tree_shared", - "mothur_dist_shared", "mothur_heatmap_sim", + "mothur_dist_shared", + "mothur_tree_shared", "newick_display" ], "update_time": "2023-11-09", @@ -5383,13 +5383,13 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "652", @@ -5423,13 +5423,13 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "651", @@ -5447,9 +5447,9 @@ ], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_sub_sample", "mothur_classify_otu", + "mothur_sub_sample", + "mothur_cluster_split", "mothur_count_groups" ], "update_time": "2023-11-09", @@ -5465,13 +5465,13 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "650", @@ -5488,8 +5488,8 @@ "metagenomics" ], "tools": [ - "mothur_remove_lineage", - "mothur_classify_seqs" + "mothur_classify_seqs", + "mothur_remove_lineage" ], "update_time": "2023-11-09", "versions": 1 @@ -5504,13 +5504,13 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "648", @@ -5527,8 +5527,8 @@ "metagenomics" ], "tools": [ - "mothur_summary_seqs", "mothur_count_seqs", + "mothur_summary_seqs", "mothur_unique_seqs", "mothur_screen_seqs" ], @@ -5545,13 +5545,13 @@ ], "doi": null, "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "649", @@ -5570,11 +5570,11 @@ "tools": [ "mothur_pre_cluster", "mothur_screen_seqs", - "mothur_remove_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", - "mothur_summary_seqs" + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_unique_seqs" ], "update_time": "2023-11-09", "versions": 1 @@ -5586,20 +5586,20 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "641", @@ -5618,22 +5618,22 @@ ], "tools": [ "", + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-10-07", "versions": 13 @@ -5645,15 +5645,15 @@ ], "doi": "10.48546/workflowhub.workflow.608.1", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", + "Genome assembly", "Sequence alignment", + "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -5674,16 +5674,16 @@ "hi-c" ], "tools": [ - "bellerophon", - "pretext_map", - "gfa_to_fa", + "bwa_mem2", "param_value_from_file", - "yahs", "merqury", - "busco", - "bwa_mem2", + "yahs", + "gfa_to_fa", + "gfastats", "pretext_snapshot", - "gfastats" + "busco", + "pretext_map", + "bellerophon" ], "update_time": "2024-03-13", "versions": 1 @@ -5716,35 +5716,35 @@ "eosc4cancer" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "snpSift_extractFields", - "__FILTER_FROM_FILE__", - "export_remote", - "split_file_to_collection", - "__BUILD_LIST__", - "vcfanno", - "ensembl_vep", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", - "snpSift_filter", - "Add_a_column1", - "datamash_transpose", + "snpSift_extractFields", "collapse_dataset", + "tp_find_and_replace", + "tp_tail_tool", + "bg_column_arrange_by_header", "add_line_to_file", + "ensembl_vep", "param_value_from_file", - "compose_text_param", + "Filter1", + "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "__BUILD_LIST__", "__SORTLIST__", - "__RELABEL_FROM_FILE__", + "bcftools_plugin_split_vep", + "tp_easyjoin_tool", + "export_remote", + "compose_text_param", "tp_replace_in_column", - "tp_tail_tool", + "__RELABEL_FROM_FILE__", + "datamash_ops", + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "snpSift_filter", "Cut1", - "bcftools_plugin_split_vep", - "vcf2maf", - "Filter1" + "__FILTER_FROM_FILE__" ], "update_time": "2023-10-27", "versions": 1 @@ -5756,15 +5756,15 @@ ], "doi": "10.48546/workflowhub.workflow.628.1", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Variant calling", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [ "Biomedical science", @@ -5785,28 +5785,28 @@ "eosc4cancer" ], "tools": [ - "samtools_view", + "__EXTRACT_DATASET__", + "trimmomatic", + "collapse_dataset", + "Grep1", "fastqc", - "split_file_to_collection", + "__APPLY_RULES__", + "qualimap_bamqc", + "samtools_calmd", + "multiqc", "__BUILD_LIST__", - "__EXTRACT_DATASET__", - "tp_replace_in_line", + "Convert characters1", + "bwa_mem", "pick_value", - "tp_text_file_with_recurring_lines", "bamleftalign", - "collapse_dataset", + "samtools_view", "compose_text_param", - "Convert characters1", - "__APPLY_RULES__", + "tp_replace_in_line", "__RELABEL_FROM_FILE__", - "qualimap_bamqc", "varscan_somatic", - "bwa_mem", - "samtools_calmd", - "trimmomatic", "samtools_rmdup", - "multiqc", - "Grep1" + "split_file_to_collection", + "tp_text_file_with_recurring_lines" ], "update_time": "2023-10-27", "versions": 1 @@ -5835,15 +5835,15 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-07-03", "versions": 11 @@ -5856,8 +5856,8 @@ "doi": null, "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "615", @@ -5899,14 +5899,14 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2024-06-24", "versions": 2 @@ -5939,31 +5939,31 @@ "eosc4cancer" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "snpSift_extractFields", - "__FILTER_FROM_FILE__", - "split_file_to_collection", - "__BUILD_LIST__", - "vcfanno", - "ensembl_vep", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", - "snpSift_filter", - "Add_a_column1", - "datamash_transpose", + "snpSift_extractFields", "collapse_dataset", + "tp_find_and_replace", + "Cut1", + "bg_column_arrange_by_header", "add_line_to_file", + "ensembl_vep", + "Filter1", + "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "__BUILD_LIST__", "__SORTLIST__", - "__RELABEL_FROM_FILE__", - "tp_replace_in_column", - "Cut1", "bcftools_plugin_split_vep", - "vcf2maf", - "Filter1" + "tp_easyjoin_tool", + "tp_replace_in_column", + "__RELABEL_FROM_FILE__", + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "snpSift_filter", + "datamash_ops", + "__FILTER_FROM_FILE__" ], "update_time": "2023-10-27", "versions": 1 @@ -5975,15 +5975,15 @@ ], "doi": "10.48546/workflowhub.workflow.605.1", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly visualisation", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [ "Whole genome sequencing" @@ -6005,13 +6005,13 @@ "hifi" ], "tools": [ - "gfa_to_fa", - "bandage_image", "param_value_from_file", "merqury", + "gfa_to_fa", + "gfastats", + "bandage_image", "busco", - "hifiasm", - "gfastats" + "hifiasm" ], "update_time": "2024-03-13", "versions": 1 @@ -6023,14 +6023,14 @@ ], "doi": null, "edam_operation": [ - "Data handling", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", "Sequence file editing", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", - "Sequence alignment" + "Genome indexing", + "Read mapping", + "Data handling" ], "edam_topic": [ "Bioinformatics" @@ -6059,16 +6059,16 @@ "workflow" ], "tools": [ - "bwa_mem", "vvv2_display", - "vadr", - "vardict_java", + "vcfutils_vcf2fq", + "seqtk_seq", "bcftools_call", "fastp", "cshl_fasta_formatter", - "seqtk_seq", - "bcftools_mpileup", - "vcfutils_vcf2fq" + "vadr", + "vardict_java", + "bwa_mem", + "bcftools_mpileup" ], "update_time": "2023-10-16", "versions": 1 @@ -6080,14 +6080,14 @@ ], "doi": null, "edam_operation": [ - "Data handling", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", "Sequence file editing", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", - "Sequence alignment" + "Genome indexing", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "517", @@ -6113,16 +6113,16 @@ "variant_calling" ], "tools": [ - "bwa_mem", "vvv2_display", - "vadr", - "vardict_java", + "vcfutils_vcf2fq", + "seqtk_seq", "bcftools_call", "fastp", "cshl_fasta_formatter", - "seqtk_seq", - "bcftools_mpileup", - "vcfutils_vcf2fq" + "vadr", + "vardict_java", + "bwa_mem", + "bcftools_mpileup" ], "update_time": "2023-10-16", "versions": 1 @@ -6147,8 +6147,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "deeptools_bigwig_average", - "__APPLY_RULES__" + "__APPLY_RULES__", + "deeptools_bigwig_average" ], "update_time": "2024-06-13", "versions": 2 @@ -6176,8 +6176,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "repeatmasker_wrapper", - "repeatmodeler" + "repeatmodeler", + "repeatmasker_wrapper" ], "update_time": "2023-10-24", "versions": 1 @@ -6236,8 +6236,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-11", "versions": 9 @@ -6251,10 +6251,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "561", @@ -6271,19 +6271,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-10-07", "versions": 10 @@ -6295,15 +6295,15 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "398", @@ -6320,13 +6320,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-10-07", "versions": 13 @@ -6338,15 +6338,15 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "397", @@ -6363,13 +6363,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-10-07", "versions": 12 @@ -6395,12 +6395,12 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "biobb_godmd_godmd_run_ext", - "biobb_godmd_godmd_prep_ext", "biobb_io_pdb_ext", - "biobb_analysis_cpptraj_convert_ext", "biobb_structure_utils_extract_chain_ext", - "biobb_structure_utils_remove_molecules_ext" + "biobb_analysis_cpptraj_convert_ext", + "biobb_godmd_godmd_run_ext", + "biobb_structure_utils_remove_molecules_ext", + "biobb_godmd_godmd_prep_ext" ], "update_time": "2023-08-11", "versions": 1 @@ -6426,22 +6426,22 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "biobb_flexserv_pcz_evecs_ext", + "biobb_io_pdb_ext", "biobb_analysis_cpptraj_rms_ext", + "biobb_flexserv_pcz_animate_ext", + "biobb_flexserv_pcz_hinges_ext", + "biobb_flexserv_bd_run_ext", "biobb_flexserv_pcz_info_ext", "biobb_flexserv_nma_run_ext", - "biobb_io_pdb_ext", - "biobb_flexserv_pcz_bfactor_ext", - "biobb_structure_utils_extract_atoms_ext", - "biobb_flexserv_pcz_collectivity_ext", - "biobb_flexserv_pcz_zip_ext", - "biobb_flexserv_pcz_stiffness_ext", "biobb_analysis_cpptraj_convert_ext", - "biobb_flexserv_pcz_animate_ext", - "biobb_flexserv_bd_run_ext", - "biobb_flexserv_dmd_run_ext", + "biobb_flexserv_pcz_zip_ext", + "biobb_structure_utils_extract_atoms_ext", "biobb_flexserv_pcz_unzip_ext", - "biobb_flexserv_pcz_hinges_ext" + "biobb_flexserv_dmd_run_ext", + "biobb_flexserv_pcz_stiffness_ext", + "biobb_flexserv_pcz_collectivity_ext", + "biobb_flexserv_pcz_evecs_ext", + "biobb_flexserv_pcz_bfactor_ext" ], "update_time": "2023-08-11", "versions": 1 @@ -6454,17 +6454,17 @@ ], "doi": null, "edam_operation": [ - "Filtering", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Read binning", "Sequence contamination filtering", - "Sequence trimming", + "Read binning", + "Sequence alignment", + "Sequencing quality control", "RNA-Seq analysis", + "Validation", + "Sequence trimming", "Genome alignment", - "SNP detection", - "Validation" + "Read mapping", + "Filtering", + "SNP detection" ], "edam_topic": [], "id": "519", @@ -6484,24 +6484,24 @@ "covid-19" ], "tools": [ - "bbtools_bbmap", - "deeptools_bam_coverage", - "snpeff_sars_cov_2", - "collapse_dataset", - "tp_awk_tool", - "read_it_and_keep", - "samtools_view", - "samtools_ampliconclip", - "tp_sed_tool", "samtools_stats", - "fastp", + "qualimap_bamqc", + "collapse_dataset", "compose_text_param", "ivar_consensus", + "fastp", + "deeptools_bam_coverage", + "ivar_variants", "multiqc", - "qualimap_bamqc", + "samtools_ampliconclip", + "tp_cat", + "tp_sed_tool", + "tp_awk_tool", "__FLATTEN__", - "ivar_variants", - "tp_cat" + "snpeff_sars_cov_2", + "samtools_view", + "read_it_and_keep", + "bbtools_bbmap" ], "update_time": "2023-06-30", "versions": 1 @@ -6511,10 +6511,10 @@ "creators": [], "doi": null, "edam_operation": [ - "Filtering", "Scatter plot plotting", - "Genome alignment", "Sequence alignment", + "Genome alignment", + "Filtering", "Box-Whisker plot plotting" ], "edam_topic": [], @@ -6536,8 +6536,8 @@ "tools": [ "artic_minion", "artic_guppyplex", - "read_it_and_keep", - "nanoplot" + "nanoplot", + "read_it_and_keep" ], "update_time": "2023-06-29", "versions": 1 @@ -6547,8 +6547,8 @@ "creators": [], "doi": null, "edam_operation": [ - "Genome visualisation", "Methylation analysis", + "Genome visualisation", "Variant calling" ], "edam_topic": [], @@ -6578,8 +6578,8 @@ "creators": [], "doi": null, "edam_operation": [ - "Quantification", "Image analysis", + "Quantification", "Parsing" ], "edam_topic": [ @@ -6605,26 +6605,26 @@ "imaging" ], "tools": [ - "cp_measure_image_area_occupied", + "cp_display_data_on_image", + "idr_download_by_ids", + "cp_relate_objects", + "cp_measure_object_size_shape", "cp_measure_granularity", "cp_export_to_spreadsheet", + "cp_mask_image", "cp_measure_object_intensity", + "cp_measure_texture", + "cp_common", + "cp_image_math", + "cp_gray_to_color", "cp_measure_image_intensity", - "cp_relate_objects", "cp_measure_image_quality", - "cp_image_math", "cp_identify_primary_objects", - "idr_download_by_ids", + "cp_measure_image_area_occupied", + "cp_save_images", "cp_cellprofiler", - "cp_measure_texture", - "cp_display_data_on_image", - "cp_gray_to_color", - "cp_measure_object_size_shape", "cp_enhance_or_suppress_features", - "cp_common", - "cp_save_images", - "cp_convert_objects_to_image", - "cp_mask_image" + "cp_convert_objects_to_image" ], "update_time": "2023-07-03", "versions": 1 @@ -6680,33 +6680,33 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "biobb_flexserv_pcz_evecs_ext", "biobb_analysis_cpptraj_rms_ext", - "zip", - "biobb_flexserv_pcz_animate_ext", + "biobb_flexdyn_prody_anm_ext", + "biobb_flexserv_pcz_info_ext", "biobb_analysis_cpptraj_mask_ext", - "biobb_gromacs_make_ndx_ext", "biobb_analysis_cpptraj_convert_ext", - "biobb_structure_utils_extract_model_ext", - "biobb_flexserv_pcz_zip_ext", - "biobb_flexserv_dmd_run_ext", + "biobb_flexserv_pcz_collectivity_ext", "biobb_analysis_gmx_cluster_ext", - "biobb_gromacs_trjcat_ext", "biobb_flexdyn_nolb_nma_ext", - "biobb_io_pdb_ext", + "biobb_flexserv_pcz_bfactor_ext", "biobb_flexserv_nma_run_ext", + "biobb_flexdyn_concoord_dist_ext", "biobb_flexdyn_concoord_disco_ext", - "biobb_flexdyn_prody_anm_ext", - "biobb_flexserv_pcz_collectivity_ext", - "biobb_flexserv_pcz_info_ext", - "biobb_flexserv_pcz_bfactor_ext", + "biobb_flexserv_dmd_run_ext", + "biobb_structure_utils_extract_model_ext", + "biobb_gromacs_make_ndx_ext", + "biobb_flexserv_pcz_hinges_ext", + "biobb_structure_utils_extract_chain_ext", + "zip", + "biobb_flexserv_pcz_zip_ext", "biobb_flexdyn_imod_imc_ext", - "biobb_flexserv_pcz_stiffness_ext", - "biobb_flexdyn_imod_imode_ext", + "biobb_flexserv_pcz_evecs_ext", + "biobb_io_pdb_ext", + "biobb_flexserv_pcz_animate_ext", "biobb_flexserv_bd_run_ext", - "biobb_flexdyn_concoord_dist_ext", - "biobb_structure_utils_extract_chain_ext", - "biobb_flexserv_pcz_hinges_ext" + "biobb_flexdyn_imod_imode_ext", + "biobb_gromacs_trjcat_ext", + "biobb_flexserv_pcz_stiffness_ext" ], "update_time": "2023-06-01", "versions": 1 @@ -6784,14 +6784,14 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n biobb_amber_cpptraj_randomize_ions_ext", - "\n biobb_amber_leap_solvate_ext", - "\n biobb_amber_leap_gen_top_ext", - "\n biobb_amber_leap_add_ions_ext", - "\n biobb_amber_sander_mdrun_ext", "\n biobb_amber_process_minout_ext", "\n biobb_amber_process_mdout_ext", - "\n biobb_amber_parmed_hmassrepartition_ext" + "\n biobb_amber_sander_mdrun_ext", + "\n biobb_amber_parmed_hmassrepartition_ext", + "\n biobb_amber_leap_add_ions_ext", + "\n biobb_amber_leap_gen_top_ext", + "\n biobb_amber_leap_solvate_ext", + "\n biobb_amber_cpptraj_randomize_ions_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -6817,24 +6817,24 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n biobb_structure_utils_extract_heteroatoms_ext", - "\n biobb_amber_leap_solvate_ext", + "\n biobb_amber_process_minout_ext", + "\n biobb_chemistry_acpype_params_ac_ext", + "\n biobb_analysis_cpptraj_rgyr_ext", + "\n biobb_analysis_cpptraj_image_ext", "\n biobb_structure_utils_remove_ligand_ext", "\n biobb_structure_utils_remove_pdb_water_ext", - "\n biobb_analysis_cpptraj_rgyr_ext", - "\n biobb_amber_leap_gen_top_ext", - "\n biobb_chemistry_babel_minimize_ext", "\n biobb_amber_pdb4amber_run_ext", - "\n biobb_amber_leap_add_ions_ext", - "\n biobb_amber_sander_mdrun_ext", - "\n biobb_chemistry_reduce_add_hydrogens_ext", - "\n biobb_amber_process_minout_ext", - "\n biobb_chemistry_acpype_params_ac_ext", + "\n biobb_io_pdb_ext", "\n biobb_amber_process_mdout_ext", - "\n biobb_analysis_cpptraj_image_ext", "\n biobb_analysis_cpptraj_rms_ext", + "\n biobb_chemistry_babel_minimize_ext", + "\n biobb_amber_sander_mdrun_ext", + "\n biobb_structure_utils_extract_heteroatoms_ext", + "\n biobb_chemistry_reduce_add_hydrogens_ext", + "\n biobb_amber_leap_add_ions_ext", + "\n biobb_amber_leap_gen_top_ext", "\n biobb_amber_amber_to_pdb_ext", - "\n biobb_io_pdb_ext" + "\n biobb_amber_leap_solvate_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -6860,18 +6860,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n biobb_amber_leap_solvate_ext", - "\n biobb_analysis_cpptraj_rgyr_ext", - "\n biobb_amber_leap_gen_top_ext", - "\n biobb_amber_pdb4amber_run_ext", - "\n biobb_amber_leap_add_ions_ext", - "\n biobb_amber_sander_mdrun_ext", "\n biobb_amber_process_minout_ext", - "\n biobb_amber_process_mdout_ext", + "\n biobb_analysis_cpptraj_rgyr_ext", "\n biobb_analysis_cpptraj_image_ext", "\n biobb_analysis_cpptraj_rms_ext", + "\n biobb_amber_pdb4amber_run_ext", + "\n biobb_io_pdb_ext", + "\n biobb_amber_process_mdout_ext", + "\n biobb_amber_sander_mdrun_ext", + "\n biobb_amber_leap_add_ions_ext", + "\n biobb_amber_leap_gen_top_ext", "\n biobb_amber_amber_to_pdb_ext", - "\n biobb_io_pdb_ext" + "\n biobb_amber_leap_solvate_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -6897,18 +6897,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n biobb_vs_fpocket_select_ext", - "\n biobb_vs_autodock_vina_run_ext", - "\n biobb_vs_extract_model_pdbqt_ext", "\n biobb_chemistry_babel_convert_ext", - "\n biobb_io_ideal_sdf_ext", - "\n biobb_vs_fpocket_run_ext", - "\n biobb_structure_utils_cat_pdb_ext", + "\n biobb_io_pdb_ext", + "\n biobb_vs_fpocket_select_ext", "\n biobb_vs_box_ext", - "\n biobb_vs_fpocket_filter_ext", "\n biobb_structure_utils_extract_molecule_ext", + "\n biobb_vs_fpocket_filter_ext", + "\n biobb_vs_autodock_vina_run_ext", + "\n biobb_vs_fpocket_run_ext", "\n biobb_structure_utils_str_check_add_hydrogens_ext", - "\n biobb_io_pdb_ext" + "\n biobb_io_ideal_sdf_ext", + "\n biobb_vs_extract_model_pdbqt_ext", + "\n biobb_structure_utils_cat_pdb_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -6934,10 +6934,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n biobb_io_ligand_ext", - "\n biobb_chemistry_babel_minimize_ext", "\n biobb_chemistry_acpype_params_gmx_ext", - "\n biobb_chemistry_babel_add_hydrogens_ext" + "\n biobb_chemistry_babel_minimize_ext", + "\n biobb_chemistry_babel_add_hydrogens_ext", + "\n biobb_io_ligand_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -6963,19 +6963,19 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "\n biobb_analysis_gmx_energy_ext", + "\n biobb_io_pdb_ext", + "\n biobb_gromacs_mdrun_ext", "\n biobb_analysis_gmx_trjconv_str_ext", - "\n biobb_gromacs_grompp_ext", "\n biobb_gromacs_editconf_ext", - "\n biobb_gromacs_mdrun_ext", - "\n biobb_gromacs_solvate_ext", - "\n biobb_gromacs_genion_ext", - "\n biobb_analysis_gmx_energy_ext", + "\n biobb_gromacs_grompp_ext", "\n biobb_analysis_gmx_rgyr_ext", - "\n biobb_gromacs_pdb2gmx_ext", + "\n biobb_gromacs_solvate_ext", "\n biobb_analysis_gmx_image_ext", + "\n biobb_gromacs_pdb2gmx_ext", "\n biobb_analysis_gmx_rms_ext", - "\n biobb_model_fix_side_chain_ext", - "\n biobb_io_pdb_ext" + "\n biobb_gromacs_genion_ext", + "\n biobb_model_fix_side_chain_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -7005,16 +7005,16 @@ "variant-analysis" ], "tools": [ - "bcftools_norm", "regexColumn1", "bcftools_merge", + "snpEff", "gemini_load", - "tp_grep_tool", + "bcftools_norm", "\n Filter1", - "snpEff", "gemini_inheritance", - "pyega3", - "\n CONVERTER_gz_to_uncompressed" + "\n CONVERTER_gz_to_uncompressed", + "tp_grep_tool", + "pyega3" ], "update_time": "2023-09-05", "versions": 2 @@ -7027,17 +7027,17 @@ ], "doi": null, "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Local alignment", - "Sequence alignment", + "Generation", "Genome indexing", - "Sequence contamination filtering", - "Global alignment", + "Sequence alignment analysis", "Sequence analysis", - "Generation", - "Validation" + "Global alignment", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "439", @@ -7055,31 +7055,31 @@ "pox" ], "tools": [ - "\n Cut1", - "samtools_view", - "fastp", - "\n __SORTLIST__", + "\n __APPLY_RULES__", "samtools_merge", - "ivar_consensus", - "split_file_to_collection", + "tp_cat", "\n __ZIP_COLLECTION__", - "\n __APPLY_RULES__", - "\n Grep1", - "tp_sed_tool", - "EMBOSS: maskseq51", - "datamash_ops", - "samtools_stats", + "\n __FLATTEN__", "\n param_value_from_file", - "\n __FILTER_FAILED_DATASETS__", - "compose_text_param", + "\n Grep1", "qualimap_bamqc", - "fasta_compute_length", - "ivar_trim", - "bwa_mem", - "\n __FLATTEN__", "collection_element_identifiers", + "EMBOSS: maskseq51", "multiqc", - "tp_cat" + "bwa_mem", + "ivar_trim", + "samtools_view", + "fasta_compute_length", + "\n Cut1", + "\n __SORTLIST__", + "compose_text_param", + "ivar_consensus", + "samtools_stats", + "fastp", + "split_file_to_collection", + "\n __FILTER_FAILED_DATASETS__", + "tp_sed_tool", + "datamash_ops" ], "update_time": "2024-06-22", "versions": 2 @@ -7106,15 +7106,15 @@ "tags": [], "tools": [ "collapse_dataset", - "rdock_sort_filter", + "compose_text_param", "ctb_frankenstein_ligand", "enumerate_charges", + "split_file_to_collection", "rxdock_rbcavity", - "rxdock_rbdock", - "sucos_docking_scoring", - "compose_text_param", + "rdock_sort_filter", "openbabel_compound_convert", - "split_file_to_collection" + "rxdock_rbdock", + "sucos_docking_scoring" ], "update_time": "2024-06-29", "versions": 4 @@ -7124,8 +7124,8 @@ "creators": [], "doi": null, "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", + "Sequencing quality control", "Genome assembly" ], "edam_topic": [], @@ -7156,12 +7156,12 @@ "creators": [], "doi": null, "edam_operation": [ - "Variant calling", "Sequence contamination filtering", + "Pairwise sequence alignment", "Read pre-processing", "Genome assembly", + "Variant calling", "Sequencing quality control", - "Pairwise sequence alignment", "Formatting" ], "edam_topic": [], @@ -7183,13 +7183,13 @@ "reads_selection" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", - "minimap2", "samtools_stats", + "minimap2", "ngsutils_bam_filter", - "shovill", + "ncbi_blastn_wrapper", "picard_SamToFastq", - "ncbi_blastn_wrapper" + "fasta_merge_files_and_filter_unique_sequences", + "shovill" ], "update_time": "2023-02-13", "versions": 1 @@ -7199,8 +7199,8 @@ "creators": [], "doi": null, "edam_operation": [ - "Data handling", - "Genome assembly" + "Genome assembly", + "Data handling" ], "edam_topic": [], "id": "434", @@ -7215,8 +7215,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "spades_rnaviralspades", - "fasterq_dump" + "fasterq_dump", + "spades_rnaviralspades" ], "update_time": "2023-02-10", "versions": 1 @@ -7228,17 +7228,17 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "395", @@ -7255,15 +7255,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", + "bowtie2", + "macs2_callpeak", "samtool_filter2", - "\n wig_to_bigWig", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "\n wig_to_bigWig", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-10-07", "versions": 14 @@ -7293,9 +7293,9 @@ "hi-c" ], "tools": [ - "cooler_csort_tabix", + "\n ", "pygenomeTracks", - "\n " + "cooler_csort_tabix" ], "update_time": "2024-10-17", "versions": 3 @@ -7307,19 +7307,19 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "399", @@ -7336,23 +7336,23 @@ "atacseq" ], "tools": [ - "\n cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", + "macs2_callpeak", + "bedtools_coveragebed", + "\n cat1", + "pe_histogram", + "samtools_idxstats", "tp_grep_tool", + "bedtools_mergebed", "multiqc", + "bedtools_bamtobed", "\n wig_to_bigWig", - "samtools_idxstats", - "macs2_callpeak", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-12-08", "versions": 19 @@ -7364,15 +7364,15 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "400", @@ -7389,17 +7389,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "\n param_value_from_file", - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", + "bamFilter", "map_param_value", "\n wig_to_bigWig", - "bamFilter", - "cutadapt" + "\n param_value_from_file", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2024-11-26", "versions": 11 @@ -7411,15 +7411,15 @@ ], "doi": null, "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "401", @@ -7436,18 +7436,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "\n param_value_from_file", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", + "bamFilter", "map_param_value", "\n wig_to_bigWig", - "bamFilter", - "cutadapt" + "\n param_value_from_file", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2024-11-19", "versions": 12 @@ -7470,8 +7470,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n sdr_mothra", - "\n save_output_rocrate" + "\n save_output_rocrate", + "\n sdr_mothra" ], "update_time": "2023-01-16", "versions": 1 @@ -7484,9 +7484,9 @@ "doi": "10.48546/workflowhub.workflow.412.1", "edam_operation": [ "Read mapping", - "RNA-Seq analysis", "Nucleic acid sequence analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "412", @@ -7501,11 +7501,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n Filter1", "htseq_count", + "bowtie2", "\n sort1", - "deseq2", - "bowtie2" + "\n Filter1", + "deseq2" ], "update_time": "2023-02-13", "versions": 1 @@ -7518,15 +7518,15 @@ ], "doi": null, "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", - "De-novo assembly", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", "Sequence assembly visualisation", - "Sequence analysis", - "Genome assembly", - "Mapping assembly" + "Mapping assembly", + "Box-Whisker plot plotting", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", + "Sequence analysis" ], "edam_topic": [ "Microbiology" @@ -7545,15 +7545,15 @@ "metagenomics" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "staramr_search", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "racon", - "unicycler" + "staramr_search" ], "update_time": "2023-02-13", "versions": 1 @@ -7578,11 +7578,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n Count1", "spocc_occ", - "\n Filter1", "\n Summary_Statistics1", - "gdal_ogr2ogr" + "\n Count1", + "gdal_ogr2ogr", + "\n Filter1" ], "update_time": "2024-12-09", "versions": 1 @@ -7612,17 +7612,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", - "\n Filter1", "compose_text_param", - "snpSift_filter" + "\n Filter1", + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2024-01-14", "versions": 5 @@ -7658,12 +7658,12 @@ "hifiasm" ], "tools": [ - "hifiadapterfilt", + "bandage_info", + "fasta-stats", "gfa_to_fa", "bandage_image", - "fasta-stats", - "hifiasm", - "bandage_info" + "hifiadapterfilt", + "hifiasm" ], "update_time": "2023-01-30", "versions": 3 @@ -7675,10 +7675,10 @@ ], "doi": "10.48546/workflowhub.workflow.237.2", "edam_operation": [ - "Scaffolding", - "Genome assembly", "Pairwise sequence alignment", - "Read binning" + "Scaffolding", + "Read binning", + "Genome assembly" ], "edam_topic": [ "Sequence assembly" @@ -7700,8 +7700,8 @@ "purge_dups" ], "tools": [ - "minimap2", "fasta-stats", + "minimap2", "purge_dups" ], "update_time": "2023-01-30", @@ -7714,10 +7714,10 @@ ], "doi": "10.48546/workflowhub.workflow.220.2", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [ "Sequence assembly" @@ -7740,8 +7740,8 @@ "qc" ], "tools": [ - "picard_SamToFastq", "fastqc", + "picard_SamToFastq", "samtools_flagstat" ], "update_time": "2023-01-30", @@ -7754,15 +7754,15 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "394", @@ -7779,13 +7779,13 @@ "chip" ], "tools": [ - "tp_grep_tool", + "bowtie2", + "macs2_callpeak", "samtool_filter2", - "\n wig_to_bigWig", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "\n wig_to_bigWig", + "tp_grep_tool" ], "update_time": "2023-12-06", "versions": 1 @@ -7811,13 +7811,13 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "\n create_metgrid_dir.cwl", - "\n metgrid.cwl", + "\n create_run_dir.cwl", "\n wrf.cwl", "\n link_grib_tool.cwl", + "\n metgrid.cwl", + "\n create_metgrid_dir.cwl", "\n real.cwl", - "\n ungrib.cwl", - "\n create_run_dir.cwl" + "\n ungrib.cwl" ], "update_time": "2023-01-16", "versions": 1 @@ -7848,14 +7848,14 @@ "validated-2022-06-29" ], "tools": [ - "\n __FILTER_FAILED_DATASETS__", - "bundle_collection", - "\n sdr_teklia_worker_htr", "\n sdr_create_sdo_from_csv", + "jq", + "\n Remove beginning1", + "bundle_collection", "\n sdr_teklia_worker_dla", + "\n sdr_teklia_worker_htr", "split_file_to_collection", - "jq", - "\n Remove beginning1" + "\n __FILTER_FAILED_DATASETS__" ], "update_time": "2023-01-16", "versions": 1 @@ -7886,13 +7886,13 @@ "validated-2022-06-29" ], "tools": [ - "\n __FILTER_FAILED_DATASETS__", - "bundle_collection", "\n sdr_create_sdo_from_csv", + "jq", + "\n Remove beginning1", + "bundle_collection", "\n sdr_teklia_worker_dla", "split_file_to_collection", - "jq", - "\n Remove beginning1" + "\n __FILTER_FAILED_DATASETS__" ], "update_time": "2023-01-16", "versions": 1 @@ -7921,16 +7921,16 @@ "default-sdr" ], "tools": [ - "\n sdr_teklia_worker_ner", - "\n ", - "\n __FILTER_FAILED_DATASETS__", - "bundle_collection", - "\n sdr_teklia_worker_htr", "\n sdr_create_sdo_from_csv", + "jq", + "\n Remove beginning1", + "bundle_collection", + "\n sdr_teklia_worker_ner", "\n sdr_teklia_worker_dla", + "\n sdr_teklia_worker_htr", + "\n __FILTER_FAILED_DATASETS__", "split_file_to_collection", - "jq", - "\n Remove beginning1" + "\n " ], "update_time": "2022-12-14", "versions": 2 @@ -7953,8 +7953,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-06-20", "versions": 1 @@ -7977,9 +7977,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "meryl", "genomescope", - "fastq_paired_end_interlacer" + "fastq_paired_end_interlacer", + "meryl" ], "update_time": "2024-06-20", "versions": 1 @@ -8012,8 +8012,8 @@ ], "doi": null, "edam_operation": [ - "Sequence analysis", - "Phylogenetic analysis" + "Phylogenetic analysis", + "Sequence analysis" ], "edam_topic": [], "id": "359", @@ -8031,10 +8031,10 @@ "phylogenomics" ], "tools": [ - "iqtree", "astral", + "clipkit", "phykit_alignment_based", - "clipkit" + "iqtree" ], "update_time": "2023-02-13", "versions": 1 @@ -8046,15 +8046,15 @@ ], "doi": null, "edam_operation": [ - "Genome assembly", - "Genetic variation analysis", - "Sequence assembly validation", "Genome annotation", - "Scaffolding", + "Genetic variation analysis", "Sequence clustering", + "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Multiple sequence alignment", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation" ], "edam_topic": [], "id": "358", @@ -8073,17 +8073,17 @@ "phylogenomics" ], "tools": [ - "collapse_dataset", "regex1", - "\n Filter1", "glimmer_gbk_to_orf", - "tp_replace_in_line", + "collapse_dataset", + "proteinortho", "proteinortho_grab_proteins", + "tp_replace_in_line", + "\n Filter1", "repeatmasker_wrapper", "busco", - "funannotate_predict", - "proteinortho", - "clustalw" + "clustalw", + "funannotate_predict" ], "update_time": "2023-02-13", "versions": 1 @@ -8095,14 +8095,14 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "357", @@ -8120,18 +8120,18 @@ "mpxv" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-10-18", "versions": 1 @@ -8164,18 +8164,18 @@ "mlxv" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", "Add_a_column1", - "gops_concat_1", - "gops_subtract_1", - "collapse_dataset", "snpSift_extractFields", - "bcftools_consensus", + "gops_subtract_1", + "gops_concat_1", "\n Cut1", - "gops_merge_1", - "\n Filter1", + "collapse_dataset", "compose_text_param", - "snpSift_filter" + "\n Filter1", + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2023-02-13", "versions": 1 @@ -8206,18 +8206,18 @@ "mpvx" ], "tools": [ - "tp_easyjoin_tool", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", + "collapse_dataset", "tp_find_and_replace", + "compose_text_param", "\n Cut1", "\n Filter1", - "datamash_ops", - "compose_text_param", "split_file_to_collection", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2023-01-16", "versions": 1 @@ -8229,14 +8229,14 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "353", @@ -8254,18 +8254,18 @@ "mpxv" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-02-13", "versions": 1 @@ -8293,8 +8293,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "stacks2_populations", - "stacks2_gstacks" + "stacks2_gstacks", + "stacks2_populations" ], "update_time": "2023-01-30", "versions": 1 @@ -8306,9 +8306,9 @@ ], "doi": null, "edam_operation": [ + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Sequence alignment" ], "edam_topic": [ "Population genomics" @@ -8326,10 +8326,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "multiqc", + "bwa_mem2", "samtools_stats", - "samtools_view", - "bwa_mem2" + "multiqc", + "samtools_view" ], "update_time": "2023-01-30", "versions": 1 @@ -8357,11 +8357,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "stacks2_cstacks", - "stacks2_gstacks", - "stacks2_populations", "stacks2_tsv2bam", - "stacks2_sstacks" + "stacks2_populations", + "stacks2_cstacks", + "stacks2_sstacks", + "stacks2_gstacks" ], "update_time": "2023-01-30", "versions": 1 @@ -8417,12 +8417,12 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "stacks2_cstacks", - "stacks2_gstacks", - "stacks2_populations", "stacks2_tsv2bam", + "stacks2_ustacks", + "stacks2_populations", + "stacks2_cstacks", "stacks2_sstacks", - "stacks2_ustacks" + "stacks2_gstacks" ], "update_time": "2023-01-30", "versions": 1 @@ -8434,9 +8434,9 @@ ], "doi": null, "edam_operation": [ + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Sequence alignment" ], "edam_topic": [ "Population genomics" @@ -8454,12 +8454,12 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "stacks2_gstacks", - "samtools_view", - "stacks2_populations", - "samtools_stats", "bwa_mem2", - "multiqc" + "samtools_stats", + "multiqc", + "stacks2_populations", + "stacks2_gstacks", + "samtools_view" ], "update_time": "2023-01-30", "versions": 1 @@ -8471,13 +8471,13 @@ ], "doi": null, "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", "Sequence contamination filtering", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Sequencing quality control", "Validation" ], "edam_topic": [ @@ -8496,10 +8496,10 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "fastqc", "fastp", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2023-01-30", "versions": 1 @@ -8511,15 +8511,15 @@ ], "doi": "10.48546/workflowhub.workflow.338.1", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Differential gene expression analysis", "Sequencing quality control", + "Sequence composition calculation", + "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "338", @@ -8534,11 +8534,11 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "bowtie2", "featurecounts", - "fastq_dump", "fastqc", - "deseq2", - "bowtie2" + "fastq_dump", + "deseq2" ], "update_time": "2023-02-13", "versions": 1 @@ -8726,28 +8726,28 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "\n biobb_md_append_ligand_ext", + "\n biobb_md_pdb2gmx_ext", + "\n biobb_md_genion_ext", + "\n biobb_structure_utils_extract_heteroatoms_ext", "\n biobb_analysis_gmx_trjconv_str_ext", - "\n biobb_md_make_ndx_ext", "\n biobb_md_solvate_ext", + "\n biobb_md_make_ndx_ext", + "\n biobb_structure_utils_cat_pdb_ext", + "\n biobb_analysis_gmx_energy_ext", + "\n biobb_chemistry_reduce_add_hydrogens_ext", + "\n biobb_analysis_gmx_image_ext", "\n biobb_model_fix_side_chain_ext", - "\n biobb_md_genion_ext", "\n biobb_md_editconf_ext", - "\n biobb_chemistry_reduce_add_hydrogens_ext", - "\n biobb_structure_utils_cat_pdb_ext", - "\n biobb_analysis_gmx_rms_ext", "\n biobb_io_pdb_ext", - "\n biobb_structure_utils_extract_heteroatoms_ext", "\n biobb_chemistry_babel_minimize_ext", - "\n biobb_md_pdb2gmx_ext", - "\n biobb_md_genrestr_ext", - "\n biobb_analysis_gmx_image_ext", - "\n biobb_structure_utils_extract_molecule_ext", - "\n biobb_md_grompp_ext", - "\n biobb_md_mdrun_ext", - "\n biobb_analysis_gmx_energy_ext", "\n biobb_analysis_gmx_rgyr_ext", "\n biobb_chemistry_acpype_params_gmx_ext", - "\n biobb_md_append_ligand_ext" + "\n biobb_md_grompp_ext", + "\n biobb_structure_utils_extract_molecule_ext", + "\n biobb_md_genrestr_ext", + "\n biobb_md_mdrun_ext", + "\n biobb_analysis_gmx_rms_ext" ], "update_time": "2023-05-03", "versions": 3 @@ -8798,29 +8798,29 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Equilibrate the system (NPT) - part 2\n biobb_md_mdrun_ext", - "Download a protein structure from the PDB database\n biobb_io_pdb_ext", - "Add Ions - part 1\n biobb_md_grompp_ext", - "Create Solvent Box\n biobb_md_editconf_ext", - "Post-processing resulting 3D trajectory - part 4\n biobb_analysis_gmx_image_ext", + "Free molecular dynamics simulation - part 2\n biobb_md_mdrun_ext", + "Post-processing resulting 3D trajectory - part 5\n biobb_analysis_gmx_trjconv_str_ext", + "Fill the box with water molecules\n biobb_md_solvate_ext", "Energetically minimize the system - part 3\n biobb_analysis_gmx_energy_ext", + "Create Solvent Box\n biobb_md_editconf_ext", + "Add Ions - part 2\n biobb_md_genion_ext", + "Post-processing resulting 3D trajectory - part 2\n biobb_analysis_gmx_rms_ext", "Equilibriate the system (NVT) - part 1\n biobb_md_grompp_ext", - "Energetically minimize the system - part 2\n biobb_md_mdrun_ext", + "Equilibrate the system (NPT) - part 2\n biobb_md_mdrun_ext", "Post-processing resulting 3D trajectory - part 3\n biobb_analysis_gmx_rgyr_ext", + "Post-processing resulting 3D trajectory - part 4\n biobb_analysis_gmx_image_ext", + "Add Ions - part 1\n biobb_md_grompp_ext", + "Energetically minimize the system - part 2\n biobb_md_mdrun_ext", "Energetically minimize the system - part 1\n biobb_md_grompp_ext", - "Post-processing resulting 3D trajectory - part 5\n biobb_analysis_gmx_trjconv_str_ext", - "Post-processing resulting 3D trajectory - part 2\n biobb_analysis_gmx_rms_ext", - "Post-processing resulting 3D trajectory - part 1\n biobb_analysis_gmx_rms_ext", - "Fill the box with water molecules\n biobb_md_solvate_ext", - "Add Ions - part 2\n biobb_md_genion_ext", - "Fix the side chains, adding any side chain atoms missing in the original structure\n biobb_model_fix_side_chain_ext", + "Equilibrate the system (NVT) - part 2\n biobb_md_mdrun_ext", "Create Protein System Topology\n biobb_md_pdb2gmx_ext", "Equilibrate the system (NPT) - part 3\n biobb_analysis_gmx_energy_ext", - "Free molecular dynamics simulation - part 1\n biobb_md_grompp_ext", - "Free molecular dynamics simulation - part 2\n biobb_md_mdrun_ext", - "Equilibrate the system (NVT) - part 2\n biobb_md_mdrun_ext", + "Download a protein structure from the PDB database\n biobb_io_pdb_ext", "Equilibrate the system (NVT) - part 3\n biobb_analysis_gmx_energy_ext", - "Equilibrate the system (NPT) - part 1\n biobb_md_grompp_ext" + "Fix the side chains, adding any side chain atoms missing in the original structure\n biobb_model_fix_side_chain_ext", + "Free molecular dynamics simulation - part 1\n biobb_md_grompp_ext", + "Equilibrate the system (NPT) - part 1\n biobb_md_grompp_ext", + "Post-processing resulting 3D trajectory - part 1\n biobb_analysis_gmx_rms_ext" ], "update_time": "2023-01-16", "versions": 1 @@ -8871,20 +8871,20 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", - "\n param_value_from_file", "gmx_solvate", - "add_line_to_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", "\n d354bc62a13564f8", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "\n param_value_from_file", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2024-07-01", "versions": 2 @@ -8909,15 +8909,15 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "ambertools_acpype", - "\n param_value_from_file", - "\n Cut1", - "tp_grep_tool", - "gmx_merge_topology_files", - "openbabel_compound_convert", "ambertools_antechamber", + "gmx_setup", + "gmx_merge_topology_files", + "\n Cut1", "ctb_rdkit_descriptors", - "gmx_setup" + "ambertools_acpype", + "openbabel_compound_convert", + "\n param_value_from_file", + "tp_grep_tool" ], "update_time": "2024-07-01", "versions": 2 @@ -8929,16 +8929,16 @@ ], "doi": null, "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "111", @@ -8958,27 +8958,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", + "\n __FLATTEN__", "\n param_value_from_file", - "\n __FILTER_FAILED_DATASETS__", - "medaka_variant", "qualimap_bamqc", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "\n __FLATTEN__", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "bedtools_intersectbed", + "\n __FILTER_FAILED_DATASETS__", + "datamash_ops" ], "update_time": "2024-06-14", "versions": 5 @@ -8991,11 +8991,11 @@ "doi": null, "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "112", @@ -9013,15 +9013,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-07-03", "versions": 3 @@ -9033,15 +9033,15 @@ ], "doi": null, "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "113", @@ -9061,17 +9061,17 @@ "iwc" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-06-29", "versions": 4 @@ -9121,10 +9121,10 @@ "segmentation" ], "tools": [ - "\n sdr_teklia_worker_dla", "jq", - "\n sdr_create_sdo", - "\n download_image" + "\n sdr_teklia_worker_dla", + "\n download_image", + "\n sdr_create_sdo" ], "update_time": "2023-01-16", "versions": 1 @@ -9152,11 +9152,11 @@ "large-genome-assembly" ], "tools": [ - "\n ae3b48869cad659b", "\n ec0fc1dbb6a13fe5", - "\n 9d0e6aba18484ea8", + "\n ae3b48869cad659b", "\n c0b5fbb61b12154d", "\n 1fbcdce7d5823b15", + "\n 9d0e6aba18484ea8", "\n 2ed2445df255451a" ], "update_time": "2023-01-16", @@ -9168,15 +9168,15 @@ "doi": null, "edam_operation": [ "DNA mapping", + "Statistical calculation", + "Sequence alignment", "Chimera detection", - "Sequence composition calculation", - "Read mapping", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping" ], "edam_topic": [ "Metagenomics" @@ -9195,28 +9195,28 @@ "metadegalaxy" ], "tools": [ - "vsearch_search", - "\n addValue", - "vsearch_chimera_detection", - "\n Cut1", - "vsearch_clustering", - "biom_convert", - "phyloseq_DESeq2", + "trimmomatic", "fastqc", "phyloseq_richness", - "phyloseq_taxonomy", - "vsearch_dereplication", - "\n cat1", - "uclust2otutable", - "samtools_fastx", + "symmetricPlot", + "vsearch_chimera_detection", + "phyloseq_net", "biom_add_metadata", - "cat_multi_datasets", - "picard_FilterSamReads", "bwa_mem", - "symmetricPlot", - "trimmomatic", + "\n cat1", + "samtools_fastx", + "\n Cut1", "phyloseq_abundance", - "phyloseq_net" + "\n addValue", + "uclust2otutable", + "vsearch_clustering", + "phyloseq_DESeq2", + "picard_FilterSamReads", + "vsearch_search", + "cat_multi_datasets", + "phyloseq_taxonomy", + "biom_convert", + "vsearch_dereplication" ], "update_time": "2024-04-17", "versions": 1 @@ -9227,16 +9227,16 @@ "doi": null, "edam_operation": [ "DNA mapping", + "Statistical calculation", + "Sequence alignment", "Chimera detection", - "Sequence merging", - "Sequence composition calculation", - "Read mapping", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping", + "Sequence merging" ], "edam_topic": [ "Metagenomics" @@ -9255,29 +9255,29 @@ "metadegalaxy" ], "tools": [ - "vsearch_search", - "\n addValue", - "vsearch_chimera_detection", - "\n Cut1", - "vsearch_clustering", - "biom_convert", - "iuc_pear", - "picard_MergeSamFiles", - "phyloseq_DESeq2", + "trimmomatic", "fastqc", "phyloseq_richness", - "phyloseq_taxonomy", - "vsearch_dereplication", - "\n cat1", - "uclust2otutable", - "samtools_fastx", + "symmetricPlot", + "vsearch_chimera_detection", + "phyloseq_net", + "picard_MergeSamFiles", "biom_add_metadata", - "picard_FilterSamReads", + "iuc_pear", "bwa_mem", - "symmetricPlot", - "trimmomatic", + "\n cat1", + "samtools_fastx", + "\n Cut1", "phyloseq_abundance", - "phyloseq_net" + "\n addValue", + "uclust2otutable", + "vsearch_clustering", + "phyloseq_DESeq2", + "picard_FilterSamReads", + "vsearch_search", + "phyloseq_taxonomy", + "biom_convert", + "vsearch_dereplication" ], "update_time": "2024-04-17", "versions": 1 @@ -9289,10 +9289,10 @@ ], "doi": "10.48546/workflowhub.workflow.229.1", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [ @@ -9361,10 +9361,10 @@ ], "doi": "10.48546/workflowhub.workflow.225.1", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", "Sequence assembly visualisation", "Mapping assembly", "Cross-assembly" @@ -9387,11 +9387,11 @@ "large-genome-assembly" ], "tools": [ + "\n barchart_gnuplot", "flye", - "bandage_image", - "quast", "fasta-stats", - "\n barchart_gnuplot" + "bandage_image", + "quast" ], "update_time": "2023-01-30", "versions": 1 @@ -9403,8 +9403,8 @@ ], "doi": "10.48546/workflowhub.workflow.224.1", "edam_operation": [ - "Sequencing quality control", - "Sequence contamination filtering" + "Sequence contamination filtering", + "Sequencing quality control" ], "edam_topic": [ "Sequence assembly" @@ -9454,8 +9454,8 @@ "large-genome-assembly" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-01-30", "versions": 1 @@ -9467,12 +9467,12 @@ ], "doi": "10.48546/workflowhub.workflow.222.1", "edam_operation": [ - "Box-Whisker plot plotting", - "Scatter plot plotting", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Scatter plot plotting", + "Validation", "Sequencing quality control", - "Validation" + "Box-Whisker plot plotting" ], "edam_topic": [ "Sequence assembly" @@ -9492,9 +9492,9 @@ "large-genome-assembly" ], "tools": [ - "fastqc", "multiqc", - "nanoplot" + "nanoplot", + "fastqc" ], "update_time": "2023-01-30", "versions": 1 @@ -9541,9 +9541,9 @@ ], "doi": "10.48546/workflowhub.workflow.226.1", "edam_operation": [ - "Variant calling", "Sequence assembly", - "Base-calling" + "Base-calling", + "Variant calling" ], "edam_topic": [ "Sequence assembly" @@ -9563,10 +9563,10 @@ "large-genome-assembly" ], "tools": [ - "\n 01041e6e0464607c", - "medaka_consensus_pipeline", + "\n d5a2cb013d9747c0", "fasta-stats", - "\n d5a2cb013d9747c0" + "\n 01041e6e0464607c", + "medaka_consensus_pipeline" ], "update_time": "2023-01-30", "versions": 1 @@ -9590,8 +9590,8 @@ "tags": [], "tools": [ "\n cbind", - "\n cbind_fileList", "\n 1d3767f98cd53029", + "\n cbind_fileList", "\n d3f11f9fc62015d5" ], "update_time": "2023-01-16", @@ -9680,13 +9680,13 @@ ], "tools": [ "symmetricPlot", + "phyloseq_DESeq2", "phyloseq_abundance", - "phyloseq_richness", + "phyloseq_net", "biom_add_metadata", - "biom_convert", "phyloseq_taxonomy", - "phyloseq_DESeq2", - "phyloseq_net" + "phyloseq_richness", + "biom_convert" ], "update_time": "2024-04-17", "versions": 1 @@ -9716,8 +9716,8 @@ ], "tools": [ "taxonomy_krona_chart", - "Kraken2Tax", - "kraken2" + "kraken2", + "Kraken2Tax" ], "update_time": "2023-02-13", "versions": 1 @@ -9747,8 +9747,8 @@ ], "tools": [ "taxonomy_krona_chart", - "Kraken2Tax", - "kraken2" + "kraken2", + "Kraken2Tax" ], "update_time": "2023-02-13", "versions": 1 @@ -9775,13 +9775,13 @@ "observation" ], "tools": [ - "tp_awk_tool", + "\n barchart_gnuplot", + "climate_stripes", "\n Filter1", + "collection_column_join", "\n csv_to_tabular", "datamash_ops", - "\n barchart_gnuplot", - "collection_column_join", - "climate_stripes" + "tp_awk_tool" ], "update_time": "2023-01-16", "versions": 1 @@ -9815,15 +9815,15 @@ "eml-annotation" ], "tools": [ - "tp_easyjoin_tool", - "datamash_transpose", "regexColumn1", - "\n Grep1", - "tp_grep_tool", - "bg_uniq", "filter_tabular", + "datamash_transpose", + "\n Remove beginning1", "regex_replace", - "\n Remove beginning1" + "tp_easyjoin_tool", + "\n Grep1", + "tp_grep_tool", + "bg_uniq" ], "update_time": "2023-11-09", "versions": 1 @@ -9833,8 +9833,8 @@ "creators": [], "doi": null, "edam_operation": [ - "Quantification", "Image analysis", + "Quantification", "Parsing" ], "edam_topic": [ @@ -9859,18 +9859,18 @@ "imaging" ], "tools": [ - "cp_common", - "cp_export_to_spreadsheet", - "cp_save_images", - "cp_measure_object_size_shape", - "cp_track_objects", - "cp_identify_primary_objects", - "cp_overlay_outlines", "unzip", - "cp_measure_object_intensity", + "cp_save_images", "cp_cellprofiler", + "cp_export_to_spreadsheet", + "cp_measure_object_intensity", "cp_tile", - "cp_color_to_gray" + "cp_track_objects", + "cp_overlay_outlines", + "cp_common", + "cp_color_to_gray", + "cp_measure_object_size_shape", + "cp_identify_primary_objects" ], "update_time": "2023-07-03", "versions": 1 @@ -9880,27 +9880,27 @@ "creators": [], "doi": null, "edam_operation": [ - "Sequence merging", - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", + "Sequence contamination filtering", + "Visualisation", "Sequence assembly", + "Database search", "Sequencing quality control", - "Pairwise sequence alignment", + "Format validation", "Formatting", - "Visualisation", + "Multiple sequence alignment", + "Conversion", + "Sequence database search", + "Sequence profile generation", "Data retrieval", - "Read pre-processing", - "Sequence contamination filtering", + "Probabilistic sequence generation", + "Sequence merging", + "Statistical calculation", "Genome assembly", - "Database search", - "Sequence profile generation", - "Format validation", - "Sequence database search", + "Pairwise sequence alignment", + "Read pre-processing", + "Sequence generation", "Variant calling", - "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment" + "Taxonomic classification" ], "edam_topic": [], "id": "100", @@ -9919,19 +9919,19 @@ "identification" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", "Kraken2Tax", - "kraken2", "flash", "minimap2", - "hmmer_hmmscan", - "fastp", - "taxonomy_krona_chart", + "kraken2", "ngsutils_bam_filter", - "shovill", - "picard_SamToFastq", "ncbi_blastn_wrapper", - "ncbi_tblastx_wrapper" + "ncbi_tblastx_wrapper", + "picard_SamToFastq", + "fastp", + "taxonomy_krona_chart", + "hmmer_hmmscan", + "fasta_merge_files_and_filter_unique_sequences", + "shovill" ], "update_time": "2023-02-13", "versions": 1 @@ -9941,13 +9941,13 @@ "creators": [], "doi": null, "edam_operation": [ - "Primer removal", + "Generation", + "Genome indexing", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "Read mapping", - "Genome indexing", - "Generation", - "Sequence alignment" + "Primer removal", + "Read mapping" ], "edam_topic": [], "id": "99", @@ -9963,9 +9963,9 @@ "tags": [], "tools": [ "samtools_fastx", + "samtool_filter2", "bwa_mem", - "trim_galore", - "samtool_filter2" + "trim_galore" ], "update_time": "2023-02-13", "versions": 1 @@ -9975,11 +9975,11 @@ "creators": [], "doi": null, "edam_operation": [ - "Aggregation", "Sequence contamination filtering", "Genome assembly", + "Sequencing quality control", "Read mapping", - "Sequencing quality control" + "Aggregation" ], "edam_topic": [], "id": "68", @@ -9996,8 +9996,8 @@ "covid-19" ], "tools": [ - "spades", "bowtie2", + "spades", "fastp", "unicycler" ], @@ -10011,11 +10011,11 @@ ], "doi": null, "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -10034,13 +10034,13 @@ "rna" ], "tools": [ - "chira_extract", + "chira_quantify", "chira_collapse", - "chira_merge", "chira_map", - "query_tabular", + "chira_extract", + "chira_merge", "fastqc", - "chira_quantify", + "query_tabular", "cutadapt" ], "update_time": "2023-02-13", @@ -10053,11 +10053,11 @@ ], "doi": null, "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -10076,13 +10076,13 @@ "rna" ], "tools": [ - "chira_extract", + "chira_quantify", "chira_collapse", - "chira_merge", "chira_map", - "query_tabular", + "chira_extract", + "chira_merge", "fastqc", - "chira_quantify", + "query_tabular", "cutadapt" ], "update_time": "2023-02-13", @@ -10134,9 +10134,9 @@ "ont" ], "tools": [ + "datamash_reverse", "tp_replace_in_line", "taxonomy_krona_chart", - "datamash_reverse", "kraken2" ], "update_time": "2023-02-13", @@ -10149,9 +10149,9 @@ ], "doi": null, "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "52", @@ -10168,10 +10168,10 @@ "ont" ], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2023-02-13", "versions": 1 @@ -10183,12 +10183,12 @@ ], "doi": null, "edam_operation": [ - "Filtering", - "De-novo assembly", - "Sequencing quality control", "Pairwise sequence alignment", + "De-novo assembly", "Genome assembly", "Mapping assembly", + "Sequencing quality control", + "Filtering", "Cross-assembly" ], "edam_topic": [], @@ -10208,11 +10208,11 @@ ], "tools": [ "flye", + "racon", + "bam_to_sam", "filtlong", "minimap2", - "nanopolish_variants", - "racon", - "bam_to_sam" + "nanopolish_variants" ], "update_time": "2023-02-13", "versions": 1 @@ -10334,28 +10334,28 @@ "creators": [], "doi": null, "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "De-novo assembly", - "Sequence annotation", - "de Novo sequencing", - "Formatting", - "Differential gene expression analysis", - "Sequencing quality control", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", "Database search", - "Sequence profile generation", "Format validation", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", "Sequence database search", + "Sequence profile generation", + "Probabilistic sequence generation", "Gene prediction", "Statistical calculation", - "Coding region prediction", - "Multiple sequence alignment", - "Validation" + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Sequence annotation", + "Sequence generation", + "De-novo assembly", + "Data retrieval", + "Validation", + "Data handling" ], "edam_topic": [], "id": "37", @@ -10377,20 +10377,20 @@ "covid-19" ], "tools": [ - "hmmer_jackhmmer", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", + "cufflinks", "gffread", - "transdecoder", - "ncbi_blastp_wrapper", - "fasterq_dump", + "hmmer_jackhmmer", "tophat2", "antismash", "fastp", - "glimmer_knowlegde-based", - "ncbi_makeblastdb", - "glimmer_build-icm", - "cufflinks", + "fasterq_dump", "multiqc", - "uniprotxml_downloader", + "ncbi_blastp_wrapper", + "transdecoder", + "glimmer_knowlegde-based", "cuffmerge" ], "update_time": "2023-02-13", @@ -10401,33 +10401,33 @@ "creators": [], "doi": null, "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "De-novo assembly", - "de Novo sequencing", - "Formatting", - "Sequencing quality control", - "Differential gene expression analysis", - "Data retrieval", "Sequence contamination filtering", - "Genome assembly", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", - "Aggregation", "Format validation", - "Read mapping", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Aggregation", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", + "Sequence profile generation", + "Probabilistic sequence generation", + "Read mapping", "Gene prediction", "Statistical calculation", - "Coding region prediction", - "Multiple sequence alignment", - "Validation" + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Genome assembly", + "Sequence generation", + "De-novo assembly", + "Generation", + "Genome indexing", + "Data retrieval", + "Validation", + "Data handling" ], "edam_topic": [], "id": "38", @@ -10449,22 +10449,22 @@ "covid-19" ], "tools": [ - "bwa_mem", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", "hmmer_jackhmmer", - "picard_MergeSamFiles", - "transdecoder", - "samtools_fastx", - "ncbi_blastp_wrapper", - "fasterq_dump", - "unicycler", "samtool_filter2", - "fastp", + "samtools_fastx", + "picard_MergeSamFiles", "antismash", - "ncbi_makeblastdb", - "glimmer_build-icm", - "glimmer_knowlegde-based", + "fastp", + "fasterq_dump", "multiqc", - "uniprotxml_downloader" + "ncbi_blastp_wrapper", + "transdecoder", + "bwa_mem", + "unicycler", + "glimmer_knowlegde-based" ], "update_time": "2023-02-13", "versions": 1 @@ -10474,34 +10474,34 @@ "creators": [], "doi": null, "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", - "Sequence annotation", - "De-novo assembly", - "de Novo sequencing", - "Formatting", - "Sequencing quality control", - "Differential gene expression analysis", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", "Format validation", - "Read mapping", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Transcriptome assembly", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", - "RNA-Seq analysis", + "Sequence profile generation", + "Probabilistic sequence generation", + "Data handling", + "Read mapping", "Gene prediction", "Statistical calculation", - "Multiple sequence alignment", + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Sequence generation", + "De-novo assembly", + "Generation", + "Genome indexing", + "Data retrieval", "Validation", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "39", @@ -10523,24 +10523,24 @@ "covid-19" ], "tools": [ - "bwa_mem", - "hmmer_jackhmmer", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", "gffread", + "samtool_filter2", + "hmmer_jackhmmer", "samtools_fastx", - "transdecoder", "stringtie_merge", - "fasterq_dump", - "ncbi_blastp_wrapper", - "samtool_filter2", - "fastp", - "hisat2", - "ncbi_makeblastdb", - "glimmer_build-icm", "antismash", + "fastp", + "fasterq_dump", "multiqc", + "ncbi_blastp_wrapper", + "transdecoder", + "bwa_mem", "glimmer_knowlegde-based", "stringtie", - "uniprotxml_downloader" + "hisat2" ], "update_time": "2023-02-13", "versions": 1 @@ -10550,32 +10550,32 @@ "creators": [], "doi": null, "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", - "Sequence annotation", - "De-novo assembly", - "Sequencing quality control", - "Formatting", - "Differential gene expression analysis", - "de Novo sequencing", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", + "Sequencing quality control", "Format validation", - "Read mapping", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", + "Data handling", + "Sequence profile generation", + "Probabilistic sequence generation", + "Read mapping", "Gene prediction", + "Sequence clustering", "Statistical calculation", - "Multiple sequence alignment", - "Validation" + "de Novo sequencing", + "Differential gene expression analysis", + "Generation", + "Genome indexing", + "De-novo assembly", + "Sequence generation", + "Data retrieval", + 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- "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "35", @@ -10705,22 +10705,22 @@ "snps" ], "tools": [ - "gatk4_mutect2", - "bwa_mem", + "bowtie2", "\n cat1", - "picard_MarkDuplicates", - "snpSift_extractFields", - "samtools_fastx", - "snpEff_build_gb", - "fasterq_dump", "snpEff", "samtool_filter2", + "snpSift_extractFields", + "samtools_fastx", + "gatk4_mutect2", + "multiqc", "fastp", + "fasterq_dump", + "picard_AddOrReplaceReadGroups", "vcfallelicprimitives", + "bwa_mem", "picard_SortSam", - "multiqc", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "snpEff_build_gb", + "picard_MarkDuplicates" ], "update_time": "2023-02-13", "versions": 1 @@ -10751,18 +10751,18 @@ "pathway prediction" ], "tools": [ - "\n rpReader", - "\n rpExtractSink", + "\n rp2paths", "\n retropath2", - "\n rpVisualiser", - "\n rpCofactors", - "\n rpFBA", + "\n rpReader", "\n rpThermo", + "\n rpExtractSink", "\n 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"source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", - "Transformation", "Univariate", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "abims_xcms_xcmsSet", "generic_filter", - "abims_xcms_group" + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "Transformation", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "corrtable", + "xcms_merge", + "Multivariate", + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11487,13 +26370,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "dc17a87057dec748", @@ -11506,25 +26389,25 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "corrtable", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", - "intens_check", - "generic_filter", - "xcms_merge", - "checkFormat", - "Transformation", - "Univariate", - "quality_metrics", - "abims_xcms_retcor", "abims_xcms_fillPeaks", - "Analytic_correlation_filtration", "Multivariate", + "xcms_merge", "abims_CAMERA_annotateDiffreport", - "Batch_correction", "Heatmap", + "abims_xcms_xcmsSet", + "checkFormat", + "msnbase_readmsdata", + "corrtable", + "intens_check", "xcms_plot_chromatogram", - "abims_xcms_group" + "generic_filter", + "quality_metrics", + "Analytic_correlation_filtration", + "Univariate", + "abims_xcms_retcor", + "Transformation", + "abims_xcms_group", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 2 @@ -11534,13 +26417,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "3c41c4c5a6332c25", @@ -11553,24 +26436,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", "intens_check", - "Batch_correction", - "checkFormat", - "quality_metrics", "Analytic_correlation_filtration", - "Transformation", "Univariate", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "abims_xcms_xcmsSet", "generic_filter", - "abims_xcms_group" + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "corrtable", + "Transformation", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "checkFormat", + "xcms_merge", + "Multivariate", + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11580,13 +26463,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "bb69fa998b900cb8", @@ -11599,24 +26482,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", + "intens_check", + "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", "msnbase_readmsdata", "corrtable", - "abims_xcms_xcmsSet", - "intens_check", - "Batch_correction", "checkFormat", - "quality_metrics", - "Analytic_correlation_filtration", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11626,13 +26509,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "15275ba7c23028ed", @@ -11645,24 +26528,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 2 @@ -11672,13 +26555,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "5964606a3836cbdf", @@ -11691,24 +26574,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11718,13 +26601,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "7cc77d6cdd8de027", @@ -11737,24 +26620,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 2 @@ -11764,13 +26647,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "180744a2f8dca6eb", @@ -11783,24 +26666,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11810,13 +26693,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "7a790b0acf8ba14d", @@ -11829,24 +26712,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 9 @@ -11856,13 +26739,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "f49e102f63d3e2bb", @@ -11875,24 +26758,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 3 @@ -11902,13 +26785,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "6895bf9cff915ba1", @@ -11921,24 +26804,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", - "Transformation", "Univariate", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "abims_xcms_xcmsSet", "generic_filter", - "abims_xcms_group" + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", + "Transformation", + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 2 @@ -11948,13 +26831,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "26bdb32c017d798c", @@ -11967,24 +26850,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-10", "versions": 4 @@ -11994,13 +26877,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "e6f26a543c3e044a", @@ -12013,24 +26896,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "checkFormat", "intens_check", - "Batch_correction", - "quality_metrics", "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "corrtable", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "Multivariate", + "xcms_merge", "Univariate", "Transformation", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-12-09", "versions": 5 @@ -12040,9 +26923,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Analysis", + "Annotation", "Deposition", - "Annotation" + "Analysis" ], "edam_topic": [], "id": "1ad87b99f0cb828c", @@ -12059,10 +26942,10 @@ "association" ], "tools": [ - "Tassel", - "Cut1", + "gwastools_manhattan_plot", "Filter1", - "gwastools_manhattan_plot" + "Cut1", + "Tassel" ], "update_time": "2024-12-06", "versions": 5 @@ -12072,13 +26955,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "49e59327f299e9f7", @@ -12096,13 +26979,13 @@ "mtbls719" ], "tools": [ - "xcms_merge", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", - "xcms_export_samplemetadata", + "abims_xcms_xcmsSet", + "msnbase_readmsdata", + "abims_xcms_group", + "xcms_merge", "generic_filter", - "abims_xcms_group" + "xcms_export_samplemetadata" ], "update_time": "2024-11-21", "versions": 7 @@ -12112,13 +26995,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "57748aa2cecf0405", @@ -12131,20 +27014,20 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", - "checkFormat", - "Batch_correction", - "quality_metrics", "Determine_BC", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "abims_xcms_xcmsSet", "generic_filter", - "abims_xcms_group" + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "checkFormat", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport", + "quality_metrics", + "Batch_correction" ], "update_time": "2024-11-03", "versions": 3 @@ -12169,16 +27052,16 @@ "tools": [ "FROGS_clustering", "FROGSSTAT_Phyloseq_Composition_Visualisation", - "FROGS_biom_to_tsv", - "FROGS_clusters_stat", - "FROGS_remove_chimera", "FROGSSTAT_Phyloseq_Alpha_Diversity", - "FROGS_taxonomic_affiliation", + "FROGS_remove_chimera", + "FROGS_preprocess", + "FROGS_affiliation_stats", + "FROGSSTAT_Phyloseq_Import_Data", "FROGSSTAT_Phyloseq_Beta_Diversity", "FROGS_Tree", - "FROGSSTAT_Phyloseq_Import_Data", - "FROGS_preprocess", - "FROGS_affiliation_stats" + "FROGS_biom_to_tsv", + "FROGS_clusters_stat", + "FROGS_taxonomic_affiliation" ], "update_time": "2024-10-24", "versions": 3 @@ -12201,9 +27084,9 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance", "FROGSSTAT_Phyloseq_Structure_Visualisation", - "FROGSSTAT_Phyloseq_Sample_Clustering" + "FROGSSTAT_Phyloseq_Sample_Clustering", + "FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" ], "update_time": "2024-10-24", "versions": 4 @@ -12228,17 +27111,17 @@ "tools": [ "FROGS_clustering", "FROGSSTAT_Phyloseq_Composition_Visualisation", + "FROGSSTAT_Phyloseq_Alpha_Diversity", "FROGS_cluster_filters", - "FROGS_biom_to_tsv", - "FROGS_clusters_stat", "FROGS_remove_chimera", - "FROGSSTAT_Phyloseq_Alpha_Diversity", - "FROGS_taxonomic_affiliation", + "FROGS_preprocess", + "FROGS_affiliation_stats", + "FROGSSTAT_Phyloseq_Import_Data", "FROGSSTAT_Phyloseq_Beta_Diversity", "FROGS_Tree", - "FROGSSTAT_Phyloseq_Import_Data", - "FROGS_preprocess", - "FROGS_affiliation_stats" + "FROGS_biom_to_tsv", + "FROGS_clusters_stat", + "FROGS_taxonomic_affiliation" ], "update_time": "2024-10-24", "versions": 18 @@ -12248,17 +27131,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence profile generation", - "Conversion", + "Statistical calculation", + "Database search", "Format validation", + "Formatting", + "Multiple sequence alignment", "Sequence generation", - "Probabilistic sequence generation", + "Conversion", "Sequence database search", - "Formatting", + "Sequence profile generation", "Data retrieval", - "Statistical calculation", - "Multiple sequence alignment", - "Database search" + "Probabilistic sequence generation" ], "edam_topic": [], "id": "7ebb54181b404733", @@ -12275,12 +27158,12 @@ "cds" ], "tools": [ - "hmm2fasta", "rbc_mafft", - "hmmsearch_db", "hmmer_hmmbuild", + "tp_cat", "trimal", - "tp_cat" + "hmm2fasta", + "hmmsearch_db" ], "update_time": "2024-10-21", "versions": 4 @@ -12308,9 +27191,9 @@ "protein" ], "tools": [ - "RapGreen", "fastatophylip", "rbc_mafft", + "RapGreen", "phyml", "trimal" ], @@ -12339,8 +27222,8 @@ "phylogenomics" ], "tools": [ - "vcf2gst", "traceancestor", + "vcf2gst", "prefilter" ], "update_time": "2024-10-01", @@ -12351,13 +27234,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "192ff9aa79217899", @@ -12374,11 +27257,11 @@ "2024" ], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "abims_xcms_group" + "msnbase_readmsdata", + "abims_xcms_group", + "xcms_merge" ], "update_time": "2024-08-03", "versions": 0 @@ -12402,11 +27285,11 @@ "tags": [], "tools": [ "FROGS_clustering", - "FROGS_clusters_stat", + "FROGS_OTU_filters", "FROGS_remove_chimera", - "FROGS_biom_to_tsv", "FROGS_preprocess", - "FROGS_OTU_filters" + "FROGS_biom_to_tsv", + "FROGS_clusters_stat" ], "update_time": "2024-07-31", "versions": 3 @@ -12416,13 +27299,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "98bb6a831a2b399d", @@ -12435,14 +27318,14 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", "abims_xcms_xcmsSet", "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport", + "generic_filter" ], "update_time": "2024-07-12", "versions": 2 @@ -12465,10 +27348,10 @@ "tools": [ "influx_si", "influx_data_manager", - "isocor", "physiofit", - "isoplot", - "physiofit_data_manager" + "isocor", + "physiofit_data_manager", + "isoplot" ], "update_time": "2024-07-12", "versions": 6 @@ -12489,17 +27372,17 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "dimet_isotopologues_plot", - "dimet_differential_analysis", + "dimet_enrichment_plot", "dimet_timecourse_analysis", - "dimet_bivariate_analysis", + "dimet_metabologram", + "dimet_isotopologues_plot", "dimet_differential_multigroup_analysis", "isocor", - "dimet_enrichment_plot", + "dimet_pca_analysis", + "dimet_bivariate_analysis", + "dimet_differential_analysis", "tracegroomer", "dimet_abundance_plot", - "dimet_metabologram", - "dimet_pca_analysis", "dimet_pca_plot" ], "update_time": "2024-05-31", @@ -12523,11 +27406,11 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2024-05-27", "versions": 9 @@ -12539,16 +27422,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Visualisation", "Sequence clustering", + "DNA barcoding", "Sequencing quality control", + "Sequence file editing", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", - "Taxonomic classification", "Sequence read processing", - "Sequence file editing", - "DNA barcoding" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "41264142d3c00016", @@ -12561,21 +27444,21 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastq_groomer", - "aligned_to_consensus", - "filter_by_fasta_ids", - "cshl_fastx_reverse_complement", - "tab2fasta", + "seqtk_trimfq", + "mothur_degap_seqs", + "fastq_to_tabular", "regex1", + "tab2fasta", "ncbi_blastn_wrapper", - "qiime_align_seqs", - "fastq_to_tabular", - "mothur_degap_seqs", + "aligned_to_consensus", "__SORTLIST__", - "seqtk_trimfq", - "mothur_merge_files", "seqtk_mergepe", - "ab1_fastq_converter" + "filter_by_fasta_ids", + "qiime_align_seqs", + "cshl_fastx_reverse_complement", + "ab1_fastq_converter", + "mothur_merge_files", + "fastq_groomer" ], "update_time": "2024-05-06", "versions": 33 @@ -12585,13 +27468,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "aa96487c5a1b29bf", @@ -12604,10 +27487,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "multiqc", - "fastqc", "stringtie", - "hisat2" + "hisat2", + "multiqc", + "fastqc" ], "update_time": "2024-04-02", "versions": 1 @@ -12619,14 +27502,14 @@ ], "doi": "", "edam_operation": [ - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation" ], "edam_topic": [], "id": "2c823ac083c3cb6d", @@ -12640,10 +27523,10 @@ "tags": [], "tools": [ "jcvi_gff_stats", - "helixer", "compleasm", - "jbrowse", - "busco" + "helixer", + "busco", + "jbrowse" ], "update_time": "2024-03-27", "versions": 4 @@ -12653,16 +27536,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Editing", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", - "RNA-Seq analysis", + "Editing", + "Scaffolding", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "55be36ab73515e65", @@ -12676,9 +27559,9 @@ "tags": [], "tools": [ "jcvi_gff_stats", + "compleasm", "helixer", "red", - "compleasm", "busco", "jbrowse" ], @@ -12690,15 +27573,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Repeat sequence detection", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation", + "Repeat sequence detection" ], "edam_topic": [], "id": "ae05ff8487f58fd6", @@ -12712,9 +27595,9 @@ "tags": [], "tools": [ "jcvi_gff_stats", + "compleasm", "helixer", "repeatmodeler", - "compleasm", "repeatmasker_wrapper", "busco", "jbrowse" @@ -12727,11 +27610,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "RNA-Seq analysis", "Nucleic acid sequence analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ff14dc4005e92cfd", @@ -12744,10 +27627,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "deseq2", + "htseq_count", "bowtie2", "fasterq_dump", - "htseq_count" + "deseq2" ], "update_time": "2024-03-06", "versions": 4 @@ -12770,11 +27653,11 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "Cut1", - "tp_sorted_uniq", "met4j_ExtractSubBipNetwork", + "tp_cat", "Grep1", - "tp_cat" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-03-04", "versions": 7 @@ -12784,13 +27667,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "b6311795ae10032b", @@ -12803,14 +27686,14 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", "abims_xcms_xcmsSet", "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport", + "generic_filter" ], "update_time": "2024-02-29", "versions": 1 @@ -12825,9 +27708,9 @@ ], "doi": "", "edam_operation": [ - "Cross-assembly", "Statistical calculation", "Expression analysis", + "Cross-assembly", "Taxonomic classification" ], "edam_topic": [], @@ -12844,8 +27727,8 @@ ], "tools": [ "recentrifuge", - "kraken2", - "est_abundance" + "est_abundance", + "kraken2" ], "update_time": "2024-01-29", "versions": 8 @@ -12858,14 +27741,14 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", - "Scaffolding", + "Genome assembly", "Sequence motif recognition", + "Multilocus sequence typing", + "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly" + "Nucleic acid feature detection" ], "edam_topic": [], "id": "7964ddc68853458f", @@ -12880,8 +27763,8 @@ "genome-annotation" ], "tools": [ - "plasmidfinder", "bakta", + "plasmidfinder", "isescan", "integron_finder" ], @@ -12893,15 +27776,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Transcriptome assembly", + "Sequence composition calculation", + "Sequence alignment analysis", "Sequence trimming", - "RNA-Seq analysis", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "334189184455d9a2", @@ -12915,12 +27798,12 @@ "tags": [], "tools": [ "sickle", - "rseqc_bam2wig", - "stringtie", "wig_to_bigWig", - "hisat2", + "rseqc_bam2wig", "fastqc", - "bamFilter" + "bamFilter", + "stringtie", + "hisat2" ], "update_time": "2024-01-18", "versions": 0 @@ -12932,16 +27815,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Visualisation", "Sequence clustering", + "DNA barcoding", "Sequencing quality control", "Phylogenetic analysis", + "Sequence file editing", "Demultiplexing", - "Visualisation", - "Taxonomic classification", "Sequence read processing", - "Sequence file editing", - "DNA barcoding" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "8b1678200a1d157a", @@ -12954,24 +27837,24 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastq_groomer", - "aligned_to_consensus", - "filter_by_fasta_ids", - "cshl_fastx_reverse_complement", "collection_element_identifiers", - "regex1", - "__FILTER_FROM_FILE__", - "tab2fasta", - "qiime_align_seqs", - "fastq_to_tabular", - "ncbi_blastn_wrapper", "unzip", "mothur_degap_seqs", "seqtk_trimfq", + "fastq_to_tabular", + "regex1", + "tab2fasta", + "ncbi_blastn_wrapper", + "aligned_to_consensus", "__SORTLIST__", - "mothur_merge_files", "seqtk_mergepe", - "ab1_fastq_converter" + "filter_by_fasta_ids", + "qiime_align_seqs", + "cshl_fastx_reverse_complement", + "ab1_fastq_converter", + "__FILTER_FROM_FILE__", + "mothur_merge_files", + "fastq_groomer" ], "update_time": "2023-12-19", "versions": 7 @@ -12999,9 +27882,9 @@ "nucleic" ], "tools": [ - "RapGreen", "fastatophylip", "rbc_mafft", + "RapGreen", "phyml", "trimal" ], @@ -13013,17 +27896,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence profile generation", - "Conversion", + "Statistical calculation", + "Database search", "Format validation", + "Formatting", + "Multiple sequence alignment", "Sequence generation", - "Probabilistic sequence generation", + "Conversion", "Sequence database search", - "Formatting", + "Sequence profile generation", "Data retrieval", - "Statistical calculation", - "Multiple sequence alignment", - "Database search" + "Probabilistic sequence generation" ], "edam_topic": [], "id": "5ec6d378e60f7ccc", @@ -13040,12 +27923,12 @@ "polypeptide" ], "tools": [ - "hmm2fasta", "rbc_mafft", - "hmmsearch_db", "hmmer_hmmbuild", + "tp_cat", "trimal", - "tp_cat" + "hmm2fasta", + "hmmsearch_db" ], "update_time": "2023-11-22", "versions": 5 @@ -13057,17 +27940,17 @@ ], "doi": "", "edam_operation": [ - "Sequence profile generation", - "Conversion", + "Statistical calculation", + "Database search", "Format validation", + "Formatting", + "Multiple sequence alignment", "Sequence generation", - "Probabilistic sequence generation", + "Conversion", "Sequence database search", - "Formatting", + "Sequence profile generation", "Data retrieval", - "Statistical calculation", - "Multiple sequence alignment", - "Database search" + "Probabilistic sequence generation" ], "edam_topic": [], "id": "d425a77157cae2ee", @@ -13084,12 +27967,12 @@ "cds" ], "tools": [ - "hmm2fasta", "rbc_mafft", - "hmmsearch_db", "hmmer_hmmbuild", + "tp_cat", "trimal", - "tp_cat" + "hmm2fasta", + "hmmsearch_db" ], "update_time": "2023-11-22", "versions": 2 @@ -13101,17 +27984,17 @@ ], "doi": "", "edam_operation": [ - "Sequence profile generation", - "Conversion", + "Statistical calculation", + "Database search", "Format validation", + "Formatting", + "Multiple sequence alignment", "Sequence generation", - "Probabilistic sequence generation", + "Conversion", "Sequence database search", - "Formatting", + "Sequence profile generation", "Data retrieval", - "Statistical calculation", - "Multiple sequence alignment", - "Database search" + "Probabilistic sequence generation" ], "edam_topic": [], "id": "b131218bec7eacb4", @@ -13128,12 +28011,12 @@ "polypeptide" ], "tools": [ - "hmm2fasta", "rbc_mafft", - "hmmsearch_db", "hmmer_hmmbuild", + "tp_cat", "trimal", - "tp_cat" + "hmm2fasta", + "hmmsearch_db" ], "update_time": "2023-11-22", "versions": 4 @@ -13145,13 +28028,13 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "32f903738292a67f", @@ -13169,13 +28052,13 @@ "w4m" ], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", "xcms_plot_chromatogram", - "xcms_export_samplemetadata", - "Multivariate" + "msnbase_readmsdata", + "Multivariate", + "xcms_merge", + "xcms_export_samplemetadata" ], "update_time": "2023-11-21", "versions": 9 @@ -13185,13 +28068,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "5ec8a143f82a8c90", @@ -13212,15 +28095,15 @@ "untargetedmetabolicprofiling" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "Batch_correction", "abims_xcms_retcor", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport", "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2023-11-19", "versions": 11 @@ -13230,12 +28113,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "0f6714dbdb90b6aa", @@ -13248,10 +28131,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastqc", - "featurecounts", "hisat2", - "collection_column_join" + "collection_column_join", + "featurecounts", + "fastqc" ], "update_time": "2023-11-16", "versions": 1 @@ -13261,12 +28144,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "72b531d980acaa6c", @@ -13279,10 +28162,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastqc", - "featurecounts", "hisat2", - "collection_column_join" + "collection_column_join", + "featurecounts", + "fastqc" ], "update_time": "2023-11-15", "versions": 11 @@ -13292,12 +28175,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "6d2945d35fa956c8", @@ -13310,10 +28193,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastqc", - "featurecounts", "hisat2", - "collection_column_join" + "collection_column_join", + "featurecounts", + "fastqc" ], "update_time": "2023-11-14", "versions": 2 @@ -13323,12 +28206,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "e0bad0b97ee71577", @@ -13341,10 +28224,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastqc", - "featurecounts", "hisat2", - "collection_column_join" + "collection_column_join", + "featurecounts", + "fastqc" ], "update_time": "2023-11-14", "versions": 5 @@ -13354,12 +28237,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "5e49933a687c2b46", @@ -13372,10 +28255,10 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "fastqc", - "featurecounts", "hisat2", - "collection_column_join" + "collection_column_join", + "featurecounts", + "fastqc" ], "update_time": "2023-11-14", "versions": 5 @@ -13385,13 +28268,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment analysis", + "Sequence alignment", "Sequence trimming", "Sequencing quality control", - "Sequence alignment" + "Data handling" ], "edam_topic": [], "id": "74b4d11c07f7f0a4", @@ -13405,11 +28288,11 @@ "tags": [], "tools": [ "sickle", - "rseqc_bam2wig", "wig_to_bigWig", - "hisat2", + "rseqc_bam2wig", "fastqc", - "bamFilter" + "bamFilter", + "hisat2" ], "update_time": "2023-10-20", "versions": 0 @@ -13468,13 +28351,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "18b2f77f2915adc7", @@ -13487,16 +28370,16 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_xcms_xcmsSet", "intens_check", - "Batch_correction", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", "checkFormat", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", "quality_metrics", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2023-07-19", "versions": 4 @@ -13519,11 +28402,11 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-05-25", "versions": 5 @@ -13535,20 +28418,20 @@ ], "doi": "", "edam_operation": [ - "Clustering", + "Chromatogram visualisation", + "Chromatographic alignment", + "Peak detection", + "Format validation", "Formatting", + "Spectral library search", + "Label-free quantification", "Mass spectrum visualisation", "Standardisation and normalisation", + "Clustering", + "Validation", "Correlation", - "Chromatogram visualisation", - "Filtering", - "Label-free quantification", - "Format validation", "Imputation", - "Chromatographic alignment", - "Peak detection", - "Spectral library search", - "Validation" + "Filtering" ], "edam_topic": [], "id": "1407c1703f360f07", @@ -13566,18 +28449,18 @@ ], "tools": [ "msconvert", - "xcms_merge", - "ramclustr", - "cat1", - "abims_xcms_fillPeaks", "metams_runGC", - "matchms_formatter", - "msnbase_readmsdata", + "cat1", + "matchms", "abims_xcms_xcmsSet", - "riassigner", "abims_xcms_retcor", + "riassigner", + "msnbase_readmsdata", "abims_xcms_group", - "matchms" + "abims_xcms_fillPeaks", + "xcms_merge", + "matchms_formatter", + "ramclustr" ], "update_time": "2023-03-24", "versions": 1 @@ -13587,13 +28470,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "4aa393a1f192a495", @@ -13606,11 +28489,11 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", "xcms_plot_chromatogram", + "msnbase_readmsdata", + "xcms_merge", "xcms_export_samplemetadata" ], "update_time": "2023-03-23", @@ -13623,13 +28506,13 @@ ], "doi": "", "edam_operation": [ + "Mass spectrum visualisation", "Chromatogram visualisation", - "Filtering", - "Label-free quantification", "Chromatographic alignment", + "Validation", "Peak detection", - "Mass spectrum visualisation", - "Validation" + "Filtering", + "Label-free quantification" ], "edam_topic": [], "id": "cca13353d553319e", @@ -13650,13 +28533,13 @@ "2023" ], "tools": [ - "mspurity_averagefragspectra", "mspurity_createdatabase", - "mspurity_frag4feature", "mspurity_filterfragspectra", + "mspurity_frag4feature", + "mspurity_puritya", "mspurity_spectralmatching", "abims_xcms_group", - "mspurity_puritya" + "mspurity_averagefragspectra" ], "update_time": "2023-03-23", "versions": 2 @@ -13666,13 +28549,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "5bfbe77fd6b37c45", @@ -13690,19 +28573,19 @@ "w4m" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "Multivariate", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", + "abims_xcms_xcmsSet", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", "checkFormat", - "Batch_correction", + "abims_xcms_group", + "abims_xcms_fillPeaks", "quality_metrics", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "xcms_merge", + "Multivariate", "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2023-03-22", "versions": 12 @@ -13712,11 +28595,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Primer removal" ], "edam_topic": [], "id": "b5d86d505c09d170", @@ -13729,14 +28612,14 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", - "dada2_seqCounts", + "dada2_plotQualityProfile", + "dada2_dada", "dada2_removeBimeraDenovo", - "dada2_mergePairs", + "dada2_seqCounts", "dada2_filterAndTrim", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "cutadapt" ], "update_time": "2023-02-15", @@ -13749,14 +28632,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "d0d12c0b80c286f9", @@ -13775,26 +28658,26 @@ "latest" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2022-06-08", "versions": 2 @@ -13807,11 +28690,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "57b5a45c9f71a09c", @@ -13829,15 +28712,15 @@ "latest" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-04-15", "versions": 3 @@ -13849,15 +28732,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "727cfdb7c79287d1", @@ -13876,20 +28759,20 @@ "artic" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-04-15", "versions": 4 @@ -13917,20 +28800,20 @@ "latest" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-04-15", "versions": 1 @@ -13960,18 +28843,18 @@ "latest" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-04-15", "versions": 1 @@ -13983,16 +28866,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "61235264d5d2f666", @@ -14012,27 +28895,27 @@ "latest" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-04-15", "versions": 1 @@ -14044,15 +28927,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "54b48eeeed3564dd", @@ -14071,17 +28954,17 @@ "latest" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-04-15", "versions": 1 @@ -14093,18 +28976,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "591c57173e259ca6", @@ -14123,21 +29006,21 @@ "latest" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-04-15", "versions": 2 @@ -14149,13 +29032,13 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "bcd348178335a19b", @@ -14175,20 +29058,20 @@ "dda" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "mspurity_averagefragspectra", - "mspurity_createmsp", - "abims_xcms_xcmsSet", + "metfrag", "mspurity_createdatabase", - "mspurity_frag4feature", "mspurity_filterfragspectra", + "mspurity_frag4feature", + "abims_xcms_xcmsSet", + "mspurity_puritya", "mspurity_spectralmatching", - "metfrag", + "msnbase_readmsdata", + "mspurity_createmsp", "abims_xcms_group", - "mspurity_puritya" + "abims_xcms_fillPeaks", + "xcms_merge", + "mspurity_averagefragspectra", + "abims_CAMERA_annotateDiffreport" ], "update_time": "2022-03-14", "versions": 5 @@ -14198,13 +29081,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "e6a55d00f1364794", @@ -14217,16 +29100,16 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "Batch_correction", - "quality_metrics", "abims_xcms_retcor", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "quality_metrics", + "xcms_merge", + "abims_CAMERA_annotateDiffreport", "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2021-12-30", "versions": 2 @@ -14236,13 +29119,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "e3d00bdef9addd7c", @@ -14255,20 +29138,20 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_xcms_summary", - "Multivariate", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", + "abims_xcms_xcmsSet", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", "checkFormat", - "Batch_correction", + "abims_xcms_group", + "abims_xcms_fillPeaks", "quality_metrics", - "xcms_plot_chromatogram", - "abims_xcms_retcor", + "xcms_merge", + "Multivariate", + "abims_xcms_summary", "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2021-12-22", "versions": 4 @@ -14280,16 +29163,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "e3c04a30258421aa", @@ -14308,27 +29191,27 @@ "emergen" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2021-11-02", "versions": 2 @@ -14340,18 +29223,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "2345fad7dac13daa", @@ -14367,21 +29250,21 @@ "covid-19" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-09-13", "versions": 5 @@ -14393,15 +29276,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bffee40c87c7b20a", @@ -14419,17 +29302,17 @@ "covid-19" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-09-13", "versions": 2 @@ -14442,11 +29325,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "ca0bd0e42cb774f9", @@ -14463,15 +29346,15 @@ "covid-19" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-09-13", "versions": 2 @@ -14498,20 +29381,20 @@ "covid-19" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2021-09-13", "versions": 3 @@ -14523,14 +29406,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "98529cff0ef36b91", @@ -14548,22 +29431,22 @@ "artic" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-09-13", "versions": 2 @@ -14592,18 +29475,18 @@ "covid-19" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2021-09-13", "versions": 2 @@ -14614,9 +29497,9 @@ "doi": "", "edam_operation": [ "Methylation analysis", - "Variant calling", + "Tree-based sequence alignment", "Variant classification", - "Tree-based sequence alignment" + "Variant calling" ], "edam_topic": [], "id": "feb57548b3ce914d", @@ -14643,9 +29526,9 @@ "doi": "", "edam_operation": [ "Methylation analysis", - "Variant calling", + "Tree-based sequence alignment", "Variant classification", - "Tree-based sequence alignment" + "Variant calling" ], "edam_topic": [], "id": "e4735d214a68b790", @@ -14673,14 +29556,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "7d27dd394b921846", @@ -14698,22 +29581,22 @@ "emergen" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-07-07", "versions": 1 @@ -14742,18 +29625,18 @@ "emergen" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2021-07-06", "versions": 1 @@ -14777,8 +29660,8 @@ "covid19.galaxyproject.org" ], "tools": [ - "__ZIP_COLLECTION__", - "collapse_dataset" + "collapse_dataset", + "__ZIP_COLLECTION__" ], "update_time": "2021-06-04", "versions": 5 @@ -14790,14 +29673,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "e0b225d4b2556365", @@ -14814,22 +29697,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-06-04", "versions": 1 @@ -14839,13 +29722,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "06fa7dd6eea42350", @@ -14862,20 +29745,20 @@ "lcms" ], "tools": [ - "xcms_merge", + "wsdl_hmdb", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "Univariate", + "abims_xcms_group", "abims_xcms_fillPeaks", + "xcms_merge", "abims_xcms_summary", "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", - "Batch_correction", - "wsdl_hmdb", "quality_metrics", - "Univariate", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2021-04-23", "versions": 4 @@ -14901,13 +29784,13 @@ "esi" ], "tools": [ - "mspurity_averagefragspectra", "mspurity_createdatabase", - "mspurity_createmsp", - "mspurity_frag4feature", "mspurity_filterfragspectra", + "mspurity_frag4feature", + "mspurity_puritya", "mspurity_spectralmatching", - "mspurity_puritya" + "mspurity_createmsp", + "mspurity_averagefragspectra" ], "update_time": "2021-04-06", "versions": 4 @@ -14917,18 +29800,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "5d83e0886f2a7465", @@ -14941,15 +29824,15 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ - "picard_MarkDuplicates", - "rseqc_read_distribution", "featurecounts", - "rseqc_infer_experiment", - "hisat2", + "cutadapt", "multiqc", "collection_column_join", "fastqc", - "cutadapt" + "hisat2", + "rseqc_infer_experiment", + "rseqc_read_distribution", + "picard_MarkDuplicates" ], "update_time": "2021-04-04", "versions": 2 @@ -14959,9 +29842,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "10073c7392914246", @@ -14984,13 +29867,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "19e99a5c09c01bb7", @@ -15003,19 +29886,19 @@ "source": "https://usegalaxy.fr", "tags": [], "tools": [ + "Analytic_correlation_filtration", + "abims_xcms_xcmsSet", + "abims_xcms_retcor", + "corrtable", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "quality_metrics", "xcms_merge", "tp_easyjoin_tool", - "abims_xcms_fillPeaks", "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "corrtable", - "abims_xcms_xcmsSet", - "Batch_correction", - "Analytic_correlation_filtration", - "quality_metrics", - "abims_xcms_retcor", "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2021-02-25", "versions": 2 @@ -15025,13 +29908,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "2ee479308227a926", @@ -15051,16 +29934,16 @@ "liquidchromatography-massspectrometry" ], "tools": [ - "xcms_merge", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "msnbase_readmsdata", + "abims_xcms_group", "abims_xcms_fillPeaks", + "xcms_merge", "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", - "Batch_correction", "quality_metrics", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2020-09-24", "versions": 3 @@ -15112,14 +29995,14 @@ "proteore" ], "tools": [ - "tp_cut_tool", - "MQoutputfilter", - "IDconverter", - "retrieve_from_hpa", - "rna_abbased_data", - "prot_features", "Jvenn", - "retr_pepatlas1" + "retr_pepatlas1", + "prot_features", + "rna_abbased_data", + "retrieve_from_hpa", + "IDconverter", + "tp_cut_tool", + "MQoutputfilter" ], "update_time": "2020-06-24", "versions": 0 @@ -15143,13 +30026,13 @@ "proteore" ], "tools": [ + "Jvenn", + "rna_abbased_data", "cluter_profiler", + "retrieve_from_hpa", "IDconverter", "MQoutputfilter", - "reactome_analysis", - "retrieve_from_hpa", - "rna_abbased_data", - "Jvenn" + "reactome_analysis" ], "update_time": "2020-06-22", "versions": 0 @@ -15173,15 +30056,15 @@ "proteore" ], "tools": [ - "tp_cut_tool", - "MQoutputfilter", - "IDconverter", + "Jvenn", + "retr_pepatlas1", + "prot_features", "sel_ann_hpa", "proteore_get_unique_peptide_srm_method", "retrieve_from_hpa", - "prot_features", - "Jvenn", - "retr_pepatlas1" + "IDconverter", + "tp_cut_tool", + "MQoutputfilter" ], "update_time": "2020-06-22", "versions": 0 @@ -15191,9 +30074,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -15209,13 +30092,13 @@ "covid-19" ], "tools": [ - "bwa_mem", - "collapse_dataset", - "snpSift_extractFields", - "snpEff_build_gb", "snpEff", "samtool_filter2", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "bwa_mem", + "snpEff_build_gb", "lofreq_call" ], "update_time": "2020-03-25", @@ -15226,15 +30109,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Statistical calculation", "Sequence alignment", "Phylogenetic tree generation (from molecular sequences)", - "Statistical calculation", - "Global alignment", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "297b71156b297a73", @@ -15249,12 +30132,12 @@ "covid-19" ], "tools": [ + "rbc_mafft", + "EMBOSS: transeq101", "fasttree", "hyphy_gard", - "EMBOSS: transeq101", - "rbc_mafft", - "hyphy_absrel", - "EMBOSS: tranalign100" + "EMBOSS: tranalign100", + "hyphy_absrel" ], "update_time": "2020-03-24", "versions": 1 @@ -15264,12 +30147,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "b3974acb70608e38", @@ -15284,8 +30167,8 @@ "covid-19" ], "tools": [ - "EMBOSS: transeq101", "rbc_mafft", + "EMBOSS: transeq101", "EMBOSS: tranalign100" ], "update_time": "2020-03-24", @@ -15296,10 +30179,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment", "Formatting", - "Phylogenetic tree generation (from molecular sequences)" + "Multiple sequence alignment" ], "edam_topic": [], "id": "c7be6e229a045fad", @@ -15314,15 +30197,15 @@ "covid-19" ], "tools": [ - "fasttree", - "ncbi_acc_download", - "collapse_dataset", "picard_NormalizeFasta", - "Cut1", - "tp_sed_tool", "rbc_mafft", + "fasttree", + "collapse_dataset", "Remove beginning1", - "Convert characters1" + "Convert characters1", + "tp_sed_tool", + "ncbi_acc_download", + "Cut1" ], "update_time": "2020-03-24", "versions": 1 @@ -15332,9 +30215,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "5bb882218afda132", @@ -15349,10 +30232,10 @@ "covid-19" ], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2020-03-22", "versions": 1 @@ -15362,20 +30245,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", "Pairwise sequence alignment", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "776ef2fa51094ba6", @@ -15390,16 +30273,16 @@ "covid-19" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "fasterq_dump", - "minimap2", "samtool_filter2", + "samtools_fastx", + "picard_MergeSamFiles", "fastp", + "fasterq_dump", + "nanoplot", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-03-22", "versions": 1 @@ -15424,13 +30307,13 @@ "introduction" ], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2024-10-17", "versions": 0 @@ -15442,20 +30325,20 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Sequence annotation", + "Genome annotation", + "Homology-based gene prediction", + "Information extraction", + "Sequence motif recognition", "Genome assembly", "Sequence alignment", "Fold recognition", - "Genome visualisation", - "Genome annotation", - "Sequence motif recognition", - "Homology-based gene prediction", + "Scaffolding", "Query and retrieval", + "Transcriptome assembly", + "Protein feature detection", "Sequence assembly validation", - "Scaffolding", - "Information extraction", - "Transcriptome assembly" + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "932f4901960a595a", @@ -15470,15 +30353,15 @@ "genome-annotation" ], "tools": [ - "interproscan", - "funannotate_annotate", + "jbrowse", "aegean_parseval", - "rna_star", "eggnog_mapper", - "jbrowse", + "interproscan", "busco", + "rna_star", "funannotate_compare", - "funannotate_predict" + "funannotate_predict", + "funannotate_annotate" ], "update_time": "2024-10-17", "versions": 0 @@ -15568,37 +30451,434 @@ "versions": 0 }, { - "create_time": "2024-12-13", + "create_time": "2024-12-20", "creators": [ - "J\u00f6rg T. Wennmann" + "B\u00e9r\u00e9nice Batut", + "G\u00e9raldine Piot" ], "doi": "", "edam_operation": [ - "Pairwise sequence alignment" + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", + "Visualisation", + "Sequencing quality control", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Formatting", + "Aggregation", + "Standardisation and normalisation", + "Species frequency estimation", + "Conversion", + "Read mapping", + "Taxonomic classification" ], "edam_topic": [], - "id": "56d1f85b0b58ed27", - "latest_version": 4, + "id": "cb2df493f5e334f7", + "latest_version": 2, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7", + "name": "Metagenomic Taxonomy and Functional Analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:metagenomics", + "microbiome", + "diversity", + "name:microgalaxy" + ], + "tools": [ + "collapse_dataset", + "humann", + "fastq_paired_end_interlacer", + "humann_unpack_pathways", + "collection_column_join", + "est_abundance", + "metaphlan", + "add_line_to_file", + "humann_regroup_table", + "bowtie2", + "collection_element_identifiers", + "humann_rename_table", + "sort1", + "krakentools_kreport2krona", + "csv_to_tabular", + "tp_easyjoin_tool", + "__UNZIP_COLLECTION__", + "krakentools_alpha_diversity", + "cat1", + "kraken2", + "taxpasta", + "tp_replace_in_line", + "taxonomy_krona_chart", + "__ZIP_COLLECTION__", + "datamash_transpose", + "fastp", + "Remove beginning1", + "tp_sed_tool", + "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "humann_renorm_table" + ], + "update_time": "2024-12-20", + "versions": 2 + }, + { + "create_time": "2024-12-20", + "creators": [ + "Subina Mehta", + "Marie Crane", + "Emma Leith", + "B\u00e9r\u00e9nice Batut", + "Saskia Hiltemann", + "Magnus \u00d8 Arntzen", + "Benoit J. Kunath", + "Phillip B. Pope", + "Francesco Delogu", + "Ray Sajulga", + "Praveen Kumar", + "James E. Johnson", + "Timothy J. Griffin", + "Pratik D. Jagtap" + ], + "doi": "", + "edam_operation": [ + "Visualisation", + "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence similarity search", + "Conversion", + "Phylogenetic inference", + "Sequence trimming", + "Statistical calculation", + "Sequence comparison", + "Phylogenetic tree editing", + "Sequence composition calculation", + "Read pre-processing", + "Sequence alignment analysis", + "Validation", + "Phylogenetic tree visualisation", + "Taxonomic classification" + ], + "edam_topic": [], + "id": "096b75501c8e0888", + "latest_version": 3, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=096b75501c8e0888", + "name": "ASaiM-MT: Metatranscriptomics Analysis of Microbes", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "asaim", + "metatranscriptomics", + "rna-seq", + "microbiome", + "name:microgalaxy" + ], + "tools": [ + "humann2_renorm_table", + "combine_metaphlan2_humann2", + "Grep1", + "fastq_paired_end_interlacer", + "metaphlan2krona", + "fastqc", + "humann2", + "multiqc", + "metaphlan2", + "group_humann2_uniref_abundances_to_go", + "humann2_genefamilies_genus_level", + "tp_sort_header_tool", + "cutadapt", + "export2graphlan", + "bg_sortmerna", + "taxonomy_krona_chart", + "humann2_unpack_pathways", + "graphlan_annotate", + "graphlan", + "Grouping1", + "format_metaphlan2_output" + ], + "update_time": "2024-12-20", + "versions": 3 + }, + { + "create_time": "2024-12-20", + "creators": [ + "B\u00e9r\u00e9nice Batut", + "Paul Zierep", + "Mina Hojat Ansari", + "Patrick B\u00fchler" + ], + "doi": "", + "edam_operation": [ + "Genome annotation", + "Read binning", + "Visualisation", + "Genome comparison", + "Sequence assembly", + "Sequencing quality control", + "Sequence assembly validation", + "Genome alignment", + "Read mapping", + "Statistical calculation", + "Sequence clustering", + "Genome assembly", + "Local alignment", + "Query and retrieval", + "Sequence composition calculation", + "Validation", + "Taxonomic classification" + ], + "edam_topic": [], + "id": "0563f58718be932d", + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", + "name": "MAGs building with individual assembly", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:fairymags", + "name:microgalaxy" + ], + "tools": [ + "fastq_paired_end_joiner", + "checkm_plot", + "checkm_lineage_wf", + "collection_column_join", + "concoct_cut_up_fasta", + "bowtie2", + "drep_dereplicate", + "samtools_sort", + "multiqc", + "concoct_merge_cut_up_clustering", + "gtdbtk_classify_wf", + "semibin", + "quast", + "__FLATTEN__", + "__UNZIP_COLLECTION__", + "concoct_extract_fasta_bins", + "metabat2", + "megahit", + "concoct", + "metabat2_jgi_summarize_bam_contig_depths", + "Fasta_to_Contig2Bin", + "coverm_genome", + "das_tool", + "maxbin2", + "concoct_coverage_table" + ], + "update_time": "2024-12-20", + "versions": 1 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Valerie C. Schiml", + "Magnus \u00d8. Arntzen", + "Francesco Delogu", + "Praveen Kumar", + "Benoit Kunath", + "B\u00e9r\u00e9nice Batut", + " Subina Mehta", + "James E. Johnson", + " Bj\u00f6rn Gr\u00fcning", + "Phillip B. Pope", + "Pratik D. Jagtap", + "Timothy J. Griffin" + ], + "doi": "", + "edam_operation": [ + "Statistical calculation", + "Primer removal", + "Sequencing quality control", + "Sequence comparison", + "Sequence similarity search", + "Read pre-processing", + "Sequence composition calculation", + "Sequence alignment analysis", + "Sequence trimming", + "Gene expression profiling" + ], + "edam_topic": [], + "id": "fd90652d475ed739", + "latest_version": 6, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", + "name": "MetaT: Metatranscriptomics data analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "metatranscriptomics", + "microbiome" + ], + "tools": [ + "kallisto_quant", + "bg_sortmerna", + "trim_galore", + "collection_column_join", + "fastqc", + "__UNZIP_COLLECTION__" + ], + "update_time": "2024-12-20", + "versions": 6 + }, + { + "create_time": "2024-12-19", + "creators": [ + "Galaxy", + "VGP" + ], + "doi": "", + "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Phasing", + "Transcriptome assembly", + "k-mer counting", + "Read pre-processing", + "De-novo assembly", + "Sequence trimming", + "Sequence assembly validation", + "Validation", + "Data handling" + ], + "edam_topic": [], + "id": "92dafb3d1c06e074", + "latest_version": 1, "license": "CC-BY-4.0", - "link": "https://usegalaxy.eu/published/workflow?id=56d1f85b0b58ed27", - "name": "Pileup to count nucleotides in SNV positions", + "link": "https://usegalaxy.eu/published/workflow?id=92dafb3d1c06e074", + "name": "Assembly-Hifi-Trio-phasing-VGP5 (release v0.4)", "number_of_steps": null, "projects": [], "source": "https://usegalaxy.eu", "tags": [ - "name:bacsnp", - "name:baculoviridae", - "name:nudivirudae", - "name:naldv", - "name:haplotype", - "name:genotype" + "vgp", + "reviewed" ], "tools": [ - "minimap2", - "samtools_mpileup" + "__EXTRACT_DATASET__", + "tp_find_and_replace", + "join1", + "tp_grep_tool", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", + "Convert characters1", + "busco", + "cutadapt", + "hifiasm", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", + "Cut1", + "tp_awk_tool" ], - "update_time": "2024-12-13", - "versions": 4 + "update_time": "2024-12-19", + "versions": 1 + }, + { + "create_time": "2024-09-08", + "creators": [ + "RECETOX" + ], + "doi": "", + "edam_operation": [ + "Feature extraction", + "Chromatographic alignment", + "Format validation", + "Peak detection", + "Spectral library search", + "Clustering", + "Standardisation and normalisation", + "Quantification", + "Alignment", + "Correlation", + "Imputation", + "Filtering" + ], + "edam_topic": [], + "id": "3086366b744e8da9", + "latest_version": 22, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=3086366b744e8da9", + "name": "GC-EI-HRMS Data Processing Workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "exposomics", + "gc-ms", + "metabolomics", + "lc-esi-ms2viadia" + ], + "tools": [ + "matchms_spectral_similarity", + "recetox_aplcms_compute_template", + "recetox_aplcms_correct_time", + "rename_annotated_feature", + "riassigner", + "recetox_aplcms_generate_feature_table", + "recetox_aplcms_align_features", + "matchms_formatter", + "waveica", + "matchms_metadata_match", + "recetox_aplcms_recover_weaker_signals", + "thermo_raw_file_converter", + "recetox_aplcms_remove_noise", + "recetox_aplcms_compute_clusters", + "ramclustr" + ], + "update_time": "2024-12-18", + "versions": 22 + }, + { + "create_time": "2024-12-17", + "creators": [], + "doi": "", + "edam_operation": [ + "Sequence composition calculation", + "Statistical calculation", + "Generation", + "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Read mapping" + ], + "edam_topic": [], + "id": "c992e77a6e8edcbd", + "latest_version": 0, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=c992e77a6e8edcbd", + "name": "SF_chr3_HW", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [], + "tools": [ + "trimmomatic", + "bcftools_call", + "snpSift_filter", + "fastqc", + "bcftools_mpileup", + "bwa", + "samtools_view", + "samtools_flagstat" + ], + "update_time": "2024-12-17", + "versions": 0 }, { "create_time": "2024-05-06", @@ -15611,7 +30891,7 @@ "edam_operation": [], "edam_topic": [], "id": "02f90a96d01fed4f", - "latest_version": 102, + "latest_version": 103, "license": "Apache-2.0", "link": "https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f", "name": "MGnify's amplicon pipeline v5.0", @@ -15621,17 +30901,51 @@ "tags": [ "mgnify_amplicon", "metagenomics", - "amplicon" + "amplicon", + "name:microgalaxy" ], "tools": [ - "fastq_dl", - "tp_awk_tool", "__MERGE_COLLECTION__", + "fastq_dl", "CONVERTER_uncompressed_to_gz", - "CONVERTER_gz_to_uncompressed" + "CONVERTER_gz_to_uncompressed", + "tp_awk_tool" + ], + "update_time": "2024-12-16", + "versions": 103 + }, + { + "create_time": "2024-12-13", + "creators": [ + "J\u00f6rg T. Wennmann" + ], + "doi": "", + "edam_operation": [ + "Pairwise sequence alignment" + ], + "edam_topic": [], + "id": "56d1f85b0b58ed27", + "latest_version": 4, + "license": "CC-BY-4.0", + "link": "https://usegalaxy.eu/published/workflow?id=56d1f85b0b58ed27", + "name": "Pileup to count nucleotides in SNV positions", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:bacsnp", + "name:baculoviridae", + "name:nudivirudae", + "name:naldv", + "name:haplotype", + "name:genotype" + ], + "tools": [ + "samtools_mpileup", + "minimap2" ], "update_time": "2024-12-13", - "versions": 102 + "versions": 4 }, { "create_time": "2024-05-17", @@ -15656,10 +30970,10 @@ "tags": [], "tools": [ "collapse_dataset", - "tp_awk_tool", - "query_tabular", + "ampvis2_load", "collection_column_join", - "ampvis2_load" + "query_tabular", + "tp_awk_tool" ], "update_time": "2024-12-12", "versions": 34 @@ -15671,16 +30985,16 @@ ], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "912b81c444e35045", @@ -15696,22 +31010,22 @@ ], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2024-12-12", "versions": 1 @@ -15732,9 +31046,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "lumpy_prep", "vcf2tsv", - "lumpy_sv" + "lumpy_sv", + "lumpy_prep" ], "update_time": "2024-12-11", "versions": 3 @@ -15761,13 +31075,13 @@ ], "tools": [ "seurat_reduce_dimension", - "Cut1", + "seurat_clustering", "seurat_preprocessing", "seurat_plot", - "csv_to_tabular", "seurat_data", - "seurat_clustering", - "seurat_create" + "seurat_create", + "csv_to_tabular", + "Cut1" ], "update_time": "2024-12-11", "versions": 7 @@ -15794,13 +31108,13 @@ ], "tools": [ "seurat_reduce_dimension", - "Cut1", + "seurat_clustering", "seurat_preprocessing", "seurat_plot", - "csv_to_tabular", "seurat_data", - "seurat_clustering", - "seurat_create" + "seurat_create", + "csv_to_tabular", + "Cut1" ], "update_time": "2024-12-11", "versions": 7 @@ -15812,13 +31126,13 @@ ], "doi": "", "edam_operation": [ - "Primer removal", + "Generation", + "Genome indexing", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "Read mapping", - "Genome indexing", - "Generation", - "Sequence alignment" + "Primer removal", + "Read mapping" ], "edam_topic": [], "id": "6223333100a9e73f", @@ -15836,68 +31150,14 @@ "name:naldv" ], "tools": [ - "bwa_mem", - "trim_galore", + "bcftools_mpileup", "bcftools_call", - "bcftools_mpileup" + "bwa_mem", + "trim_galore" ], "update_time": "2024-12-07", "versions": 5 }, - { - "create_time": "2024-09-08", - "creators": [ - "RECETOX" - ], - "doi": "", - "edam_operation": [ - "Clustering", - "Filtering", - "Format validation", - "Feature extraction", - "Imputation", - "Standardisation and normalisation", - "Quantification", - "Peak detection", - "Chromatographic alignment", - "Alignment", - "Correlation", - "Spectral library search" - ], - "edam_topic": [], - "id": "3086366b744e8da9", - "latest_version": 1, - "license": "MIT", - "link": "https://usegalaxy.eu/published/workflow?id=3086366b744e8da9", - "name": "GC-EI-HRMS Annotation Workflow (imported from URL)", - "number_of_steps": null, - "projects": [], - "source": "https://usegalaxy.eu", - "tags": [ - "exposomics", - "gc-ms", - "metabolomics", - "lc-esi-ms2viadia" - ], - "tools": [ - "ramclustr", - "matchms_spectral_similarity", - "recetox_aplcms_recover_weaker_signals", - "matchms_formatter", - "recetox_aplcms_generate_feature_table", - "waveica", - "rename_annotated_feature", - "recetox_aplcms_compute_template", - "recetox_aplcms_compute_clusters", - "recetox_aplcms_correct_time", - "riassigner", - "matchms_metadata_match", - "recetox_aplcms_remove_noise", - "recetox_aplcms_align_features" - ], - "update_time": "2024-12-06", - "versions": 1 - }, { "create_time": "2024-12-03", "creators": [ @@ -15905,9 +31165,9 @@ ], "doi": "", "edam_operation": [ - "Multiple sequence alignment", + "Phylogenetic tree generation", "Sequence alignment analysis", - "Phylogenetic tree generation" + "Multiple sequence alignment" ], "edam_topic": [], "id": "a2c46deea34d9d80", @@ -15923,20 +31183,20 @@ "name:microgalaxy" ], "tools": [ + "regexColumn1", "cat1", - "tp_split_on_column", + "Filter1", "Add_a_column1", - "regexColumn1", + "rbc_mafft", "collapse_dataset", - "join1", - "Cut1", "tab2fasta", + "bg_diamond_view", "rapidnj", - "rbc_mafft", "bg_diamond", - "bg_diamond_view", - "Filter1", - "gops_intersect_1" + "gops_intersect_1", + "join1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-12-05", "versions": 2 @@ -15949,20 +31209,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "95f420d8856bf725", @@ -15978,25 +31238,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -16009,20 +31269,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "8be366ad6a42408b", @@ -16038,25 +31298,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -16068,19 +31328,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "4daa0c33d6d50379", @@ -16095,27 +31355,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -16125,9 +31385,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Genetic variation analysis", "Genome visualisation", "Sequence analysis", - "Genetic variation analysis", "Sequence annotation" ], "edam_topic": [], @@ -16145,25 +31405,25 @@ "apollo" ], "tools": [ - "edu.tamu.cpt.genbank.shinefind", - "edu.tamu.cpt.external.aragorn-gff3", - "metagene_annotator", - "edu.tamu.cpt.gff3.fixsixpack", - "edu.tamu.cpt.fasta.remove_desc", + "edu.tamu.cpt.gff3.cdsParents", "iframe", - "jbrowse", - "get_orfs_or_cdss", - "edu.tamu.cpt.gff3.require_phage_start", - "edu.tamu.cpt2.util.glimmer3_to_gff3", "cshl_fasta_formatter", - "edu.tamu.cpt.gff3.remove_annots", + "edu.tamu.cpt.fasta.remove_desc", "create_or_update", + "edu.tamu.cpt.gff3.require_phage_start", + "get_orfs_or_cdss", "glimmer_not_knowledge_based", + "edu.tamu.cpt.gff3.remove_annots", + "edu.tamu.cpt.gff3.fixsixpack", + "filter_tabular", + "edu.tamu.cpt.genbank.shinefind", + "edu.tamu.cpt.gff3.prepForApollo", + "edu.tamu.cpt2.util.glimmer3_to_gff3", + "metagene_annotator", "aragorn_trna", "edu.tamu.cpt2.util.mga_to_gff3", - "edu.tamu.cpt.gff3.cdsParents", - "filter_tabular", - "edu.tamu.cpt.gff3.prepForApollo" + "edu.tamu.cpt.external.aragorn-gff3", + "jbrowse" ], "update_time": "2024-12-03", "versions": 5 @@ -16198,14 +31458,14 @@ "tools": [ "gbk_to_orf", "cat1", - "ncbi_acc_download", + "ncbi_makeblastdb", "fasta_filter_by_length", - "collapse_dataset", - "fastq_dump", + "fastq_to_fasta_python", "sort1", - "ncbi_makeblastdb", + "collapse_dataset", "ncbi_blastn_wrapper", - "fastq_to_fasta_python", + "ncbi_acc_download", + "fastq_dump", "fasta_compute_length" ], "update_time": "2024-11-29", @@ -16231,17 +31491,17 @@ "name:clinicalmp" ], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2024-11-28", "versions": 1 @@ -16269,8 +31529,8 @@ "name:clinicalmp" ], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2024-11-28", @@ -16283,10 +31543,10 @@ ], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -16330,16 +31590,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", - "tp_awk_tool", "collection_element_identifiers", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "decoupler_pseudobulk", + "tp_awk_tool" ], "update_time": "2024-11-28", "versions": 1 @@ -16352,10 +31612,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16370,10 +31630,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-11-28", "versions": 1 @@ -16410,14 +31670,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "2fa2f67603772413", @@ -16439,12 +31699,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-11-28", "versions": 1 @@ -16459,12 +31719,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "7e48134082dab0a3", @@ -16485,13 +31745,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-11-28", "versions": 1 @@ -16504,10 +31764,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16522,8 +31782,8 @@ "tags": [], "tools": [ "qiime2__metadata__tabulate", - "qiime2__dada2__denoise_paired", "qiime2__feature_table__tabulate_seqs", + "qiime2__dada2__denoise_paired", "qiime2__feature_table__summarize" ], "update_time": "2024-11-28", @@ -16537,10 +31797,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16570,10 +31830,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16589,8 +31849,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-11-28", @@ -16604,10 +31864,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16623,8 +31883,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-11-28", @@ -16638,10 +31898,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16656,8 +31916,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_paired", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-11-28", "versions": 1 @@ -16670,10 +31930,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -16688,8 +31948,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-11-28", "versions": 1 @@ -16702,14 +31962,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "deec04097a871646", @@ -16725,13 +31985,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-28", @@ -16748,11 +32008,11 @@ "edam_operation": [ "Sequence contamination filtering", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Sequence trimming", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "b7166aff73e5d81c", @@ -16766,17 +32026,18 @@ "tags": [ "mgnify_amplicon", "amplicon", - "metagenomics" + "metagenomics", + "name:microgalaxy" ], "tools": [ - "prinseq", + "fastq_filter", + "fastq_to_fasta_python", "trimmomatic", "tp_find_and_replace", - "fastq_filter", - "cshl_fasta_formatter", + "prinseq", "multiqc", - "fastqc", - "fastq_to_fasta_python" + "cshl_fasta_formatter", + "fastqc" ], "update_time": "2024-11-26", "versions": 16 @@ -16788,15 +32049,15 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "1fe02012c96b731f", @@ -16809,13 +32070,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "samtools_stats", - "hisat2", + "featurecounts", "multiqc", + "__FLATTEN__", "fastqc", - "deseq2", - "__FLATTEN__" + "hisat2", + "deseq2" ], "update_time": "2024-11-25", "versions": 8 @@ -16836,9 +32097,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "interpolation_run_idw_interpolation", "graphicsmagick_image_compare", "Filter1", - "interpolation_run_idw_interpolation", "tabular_to_csv" ], "update_time": "2024-11-25", @@ -16852,13 +32113,13 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "ca9d3233b0912765", @@ -16878,13 +32139,13 @@ "name:transcriptomics" ], "tools": [ - "fastqc", - "__FILTER_FAILED_DATASETS__", - "rna_star", "featurecounts", "multiqc", + "__FILTER_FAILED_DATASETS__", + "umi_tools_extract", "collection_column_join", - "umi_tools_extract" + "fastqc", + "rna_star" ], "update_time": "2024-11-24", "versions": 43 @@ -16902,20 +32163,20 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Conversion", - "Species frequency estimation", - "Phylogenetic tree analysis", - "Read mapping", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", + "Visualisation", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", "Formatting", + "Aggregation", "Standardisation and normalisation", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Nucleic acid sequence analysis" + "Species frequency estimation", + "Conversion", + "Read mapping", + "Taxonomic classification" ], "edam_topic": [], "id": "b14845359b702444", @@ -16932,37 +32193,37 @@ "diversity" ], "tools": [ - "tp_easyjoin_tool", + "collapse_dataset", "humann", "fastq_paired_end_interlacer", - "taxpasta", - "taxonomy_krona_chart", - "fastp", + "humann_unpack_pathways", + "collection_column_join", + "est_abundance", + "metaphlan", + "add_line_to_file", + "humann_regroup_table", + "bowtie2", + "collection_element_identifiers", + "humann_rename_table", + "sort1", + "krakentools_kreport2krona", + "csv_to_tabular", + "tp_easyjoin_tool", "__UNZIP_COLLECTION__", "krakentools_alpha_diversity", - "humann_rename_table", - "metaphlan", - "tp_sed_tool", + "cat1", + "kraken2", + "taxpasta", "tp_replace_in_line", - "sort1", - "tp_text_file_with_recurring_lines", + "taxonomy_krona_chart", "__ZIP_COLLECTION__", "datamash_transpose", - "collapse_dataset", - "add_line_to_file", - "humann_renorm_table", - "cat1", - "kraken2", - "tp_awk_tool", - "collection_element_identifiers", - "est_abundance", - "humann_regroup_table", + "fastp", "Remove beginning1", - "humann_unpack_pathways", - "csv_to_tabular", - "collection_column_join", - "bowtie2", - "krakentools_kreport2krona" + "tp_sed_tool", + "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "humann_renorm_table" ], "update_time": "2024-11-22", "versions": 1 @@ -16997,11 +32258,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2024-11-21", "versions": 40 @@ -17034,10 +32295,10 @@ ], "tools": [ "__EXTRACT_DATASET__", - "__FILTER_EMPTY_DATASETS__", - "map_param_value", "__BUILD_LIST__", - "Grep1" + "Grep1", + "map_param_value", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2024-11-21", "versions": 5 @@ -17062,23 +32323,23 @@ ], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence composition calculation", - "Sequence similarity search", + "Visualisation", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence comparison", - "Visualisation", + "Sequence similarity search", + "Conversion", "Phylogenetic inference", + "Sequence trimming", "Statistical calculation", - "Primer removal", - "Taxonomic classification", + "Sequence comparison", + "Phylogenetic tree editing", + "Sequence composition calculation", "Read pre-processing", - "Phylogenetic tree visualisation", - "Sequence trimming", + "Sequence alignment analysis", "Validation", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "d05c6f0f3205fbd2", @@ -17096,27 +32357,27 @@ "microbiome" ], "tools": [ + "humann2_renorm_table", "combine_metaphlan2_humann2", - "graphlan", + "Grep1", "fastq_paired_end_interlacer", - "taxonomy_krona_chart", - "fastqc", - "group_humann2_uniref_abundances_to_go", "metaphlan2krona", + "fastqc", + "humann2", + "multiqc", "metaphlan2", - "graphlan_annotate", - "humann2_renorm_table", - "Grouping1", - "bg_sortmerna", - "tp_sort_header_tool", + "group_humann2_uniref_abundances_to_go", "humann2_genefamilies_genus_level", - "humann2", + "tp_sort_header_tool", + "cutadapt", "export2graphlan", + "bg_sortmerna", + "taxonomy_krona_chart", "humann2_unpack_pathways", - "format_metaphlan2_output", - "multiqc", - "Grep1", - "cutadapt" + "graphlan_annotate", + "graphlan", + "Grouping1", + "format_metaphlan2_output" ], "update_time": "2024-11-21", "versions": 28 @@ -17132,11 +32393,11 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", "Visualisation", "Prediction and recognition", - "Formatting" + "Filtering", + "Formatting", + "Label-free quantification" ], "edam_topic": [], "id": "cd675ab32d3e7833", @@ -17153,17 +32414,17 @@ ], "tools": [ "msconvert", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", "regex1", + "query_tabular", "unipept", "tp_replace_in_line", + "search_gui", "Remove beginning1", - "query_tabular", + "tp_replace_in_column", "flashlfq", - "Filter1", - "tp_replace_in_column" + "Cut1", + "peptide_shaker" ], "update_time": "2024-11-21", "versions": 1 @@ -17180,16 +32441,16 @@ ], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "e5a89ef7b5f1c1d9", @@ -17205,12 +32466,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2024-11-21", "versions": 3 @@ -17223,19 +32484,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Validation", - "Sequence composition calculation", - "Sequencing quality control", "Visualisation", - "Analysis", "Statistical calculation", + "Analysis", "Primer removal", - "Taxonomic classification", + "Sequencing quality control", + "DNA barcoding", + "Aggregation", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "Validation", "Sequence feature detection", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "466bdd8ba7b67264", @@ -17253,21 +32514,21 @@ "name:pallori" ], "tools": [ - "ampvis2_load", - "trimmomatic", - "kraken2", - "tp_cut_tool", + "ampvis2_heatmap", "ampvis2_ordinate", "unzip", + "kraken2", + "trimmomatic", + "krakentools_kreport2krona", + "multiqc", "taxonomy_krona_chart", + "ampvis2_load", "collection_column_join", - "multiqc", - "lotus2", - "fastqc", "__FLATTEN__", - "krakentools_kreport2krona", + "fastqc", + "tp_cut_tool", "cutadapt", - "ampvis2_heatmap" + "lotus2" ], "update_time": "2024-11-21", "versions": 70 @@ -17282,10 +32543,10 @@ ], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Read mapping", "Expression analysis", - "Cross-assembly" + "Read mapping", + "Cross-assembly", + "Taxonomic classification" ], "edam_topic": [], "id": "c09159d7aad0f264", @@ -17302,70 +32563,16 @@ "name:microgalaxy" ], "tools": [ - "seq_filter_by_id", - "kraken2", + "bowtie2", "fastq_to_tabular", "filter_tabular", - "bowtie2", - "recentrifuge" + "recentrifuge", + "kraken2", + "seq_filter_by_id" ], "update_time": "2024-11-21", "versions": 2 }, - { - "create_time": "2024-11-21", - "creators": [ - "Valerie C. Schiml", - "Magnus \u00d8. Arntzen", - "Francesco Delogu", - "Praveen Kumar", - "Benoit Kunath", - "B\u00e9r\u00e9nice Batut", - " Subina Mehta", - "James E. Johnson", - " Bj\u00f6rn Gr\u00fcning", - "Phillip B. Pope", - "Pratik D. Jagtap", - "Timothy J. Griffin" - ], - "doi": "", - "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Gene expression profiling", - "Sequencing quality control", - "Sequence comparison", - "Primer removal", - "Read pre-processing", - "Sequence trimming", - "Statistical calculation" - ], - "edam_topic": [], - "id": "fd90652d475ed739", - "latest_version": 5, - "license": "MIT", - "link": "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", - "name": "Metatranscriptomics data analysis", - "number_of_steps": null, - "projects": [], - "source": "https://usegalaxy.eu", - "tags": [ - "name:microgalaxy", - "metatranscriptomics", - "microbiome" - ], - "tools": [ - "bg_sortmerna", - "trim_galore", - "__UNZIP_COLLECTION__", - "kallisto_quant", - "collection_column_join", - "fastqc" - ], - "update_time": "2024-11-21", - "versions": 5 - }, { "create_time": "2024-11-21", "creators": [ @@ -17376,11 +32583,11 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", - "Read mapping", - "Sequencing quality control", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control", + "Read mapping", + "Read summarisation" ], "edam_topic": [], "id": "63478edcea3f449a", @@ -17397,8 +32604,8 @@ "name:microgalaxy" ], "tools": [ - "multiqc", "bowtie2", + "multiqc", "featurecounts" ], "update_time": "2024-11-21", @@ -17414,10 +32621,10 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "1ef76b7b86e15792", @@ -17434,9 +32641,9 @@ "name:microgalaxy" ], "tools": [ - "fastqc", + "trimmomatic", "multiqc", - "trimmomatic" + "fastqc" ], "update_time": "2024-11-21", "versions": 6 @@ -17463,16 +32670,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", - "tp_awk_tool", "collection_element_identifiers", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "decoupler_pseudobulk", + "tp_awk_tool" ], "update_time": "2024-11-21", "versions": 1 @@ -17484,8 +32691,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "95c4d5549e820d88", @@ -17501,20 +32708,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-21", "versions": 1 @@ -17526,8 +32733,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "a9469155eee12ff1", @@ -17543,20 +32750,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-21", "versions": 1 @@ -17568,10 +32775,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "dc8b78d093be59ae", @@ -17585,12 +32792,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-11-21", "versions": 1 @@ -17603,14 +32810,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "96c61a584cb2e5e9", @@ -17626,15 +32833,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-21", "versions": 1 @@ -17647,14 +32854,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "aff44f1665a14e23", @@ -17670,15 +32877,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-21", "versions": 1 @@ -17691,14 +32898,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "b426e137396acb14", @@ -17714,13 +32921,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-21", @@ -17731,8 +32938,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Differential gene expression analysis", - "Gene-set enrichment analysis" + "Gene-set enrichment analysis", + "Differential gene expression analysis" ], "edam_topic": [], "id": "c3a11e1ac1aa8383", @@ -17745,19 +32952,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", "collection_element_identifiers", - "fgsea", "param_value_from_file", - "tp_replace_in_line", - "oncoenrichr_wrapper", - "query_tabular", "filter_tabular", + "edger", + "fgsea", + "column_remove_by_header", + "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "oncoenrichr_wrapper", + "decoupler_pseudobulk", + "query_tabular" ], "update_time": "2024-11-18", "versions": 2 @@ -17780,22 +32987,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ncbi_acc_download", - "bedtools_complementbed", - "collapse_dataset", - "gff2bed1", - "tmhmm2", "regexColumn1", - "Cut1", + "tmhmm2", + "Filter1", "fasta_filter_by_length", - "tp_replace_in_line", - "bedtools_getfastabed", - "bedtools_sortbed", + "collapse_dataset", "alphafold", - "Filter1", - "fasta_compute_length", + "tp_replace_in_line", "deepsig", - "tp_cat" + "tp_cat", + "bedtools_complementbed", + "bedtools_sortbed", + "gff2bed1", + "ncbi_acc_download", + "Cut1", + "bedtools_getfastabed", + "fasta_compute_length" ], "update_time": "2024-11-18", "versions": 3 @@ -17837,10 +33044,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence alignment", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "8edf456f4aeddaac", @@ -17853,8 +33060,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "bwa_mem2" + "bwa_mem2", + "fastqc" ], "update_time": "2024-11-14", "versions": 1 @@ -17877,12 +33084,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "CONVERTER_interval_to_bedstrict_0", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "CONVERTER_interval_to_bedstrict_0", + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-11-12", "versions": 0 @@ -17909,16 +33116,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", - "tp_awk_tool", "collection_element_identifiers", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "decoupler_pseudobulk", + "tp_awk_tool" ], "update_time": "2024-11-11", "versions": 31 @@ -17969,17 +33176,17 @@ "name:clinicalmp" ], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2024-11-05", "versions": 16 @@ -18023,11 +33230,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-11-03", "versions": 0 @@ -18037,18 +33244,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "88064e2231165fd2", @@ -18061,17 +33268,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", "samtools_calmd", - "picard_MarkDuplicates", - "vcffilter2", "varscan_somatic", "snpEff", "multiqc", + "vcffilter2", + "snpSift_filter", + "bwa_mem", "fastqc", "bamFilter", - "snpSift_filter" + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2024-11-02", "versions": 10 @@ -18081,13 +33288,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "Sequencing quality control", - "Sequence alignment" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "06fe33c4420906bf", @@ -18101,15 +33308,15 @@ "tags": [], "tools": [ "deeptools_bam_coverage", - "fastqc", - "rna_star", + "bam_to_sam", + "umi_tools_extract", "tp_awk_tool", "umi_tools_dedup", - "__UNZIP_COLLECTION__", - "umi_tools_extract", "sam_to_bam", + "fastqc", + "rna_star", "cutadapt", - "bam_to_sam" + "__UNZIP_COLLECTION__" ], "update_time": "2024-11-01", "versions": 15 @@ -18121,14 +33328,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "c084c2009f6b2d0a", @@ -18145,19 +33352,19 @@ "haploid" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "collapse_dataset", - "tp_awk_tool", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "fastp", + "multiqc", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-10-31", "versions": 1 @@ -18190,24 +33397,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-10-31", "versions": 1 @@ -18222,16 +33429,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "6b69ab27c565257b", @@ -18251,12 +33458,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-31", "versions": 1 @@ -18271,14 +33478,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "0abd32dbc5207b88", @@ -18300,12 +33507,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-31", "versions": 1 @@ -18320,12 +33527,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "0404013d5c27210d", @@ -18346,13 +33553,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-10-31", "versions": 1 @@ -18368,8 +33575,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "b203dec6ee6da2fd", @@ -18393,10 +33600,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-31", "versions": 1 @@ -18423,15 +33630,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18458,15 +33665,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18493,15 +33700,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18528,15 +33735,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18563,15 +33770,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18598,15 +33805,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18633,15 +33840,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18668,15 +33875,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18703,15 +33910,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18738,15 +33945,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-10-31", "versions": 1 @@ -18759,9 +33966,9 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", "Genome visualisation", - "Sequence motif recognition" + "Sequence motif recognition", + "Protein feature detection" ], "edam_topic": [], "id": "0b9071d5dfa38559", @@ -18778,26 +33985,26 @@ "apollo" ], "tools": [ - "edu.tamu.cpt.fasta.remove_desc", + "edu.tamu.cpt.gff3.cdsParents", "iframe", - "jbrowse", "blastxml_to_gapped_gff3", - "get_orfs_or_cdss", - "edu.tamu.cpt.gff3.require_phage_start", - "fetch_jbrowse", - "ncbi_blastp_wrapper", - "cshl_fasta_formatter", "edu.tamu.cpt.fasta.lipory", - "edu.tamu.cpt.gff3.remove_annots", - "interproscan", + "cshl_fasta_formatter", + "edu.tamu.cpt.fasta.remove_desc", "create_or_update", - "edu.tamu.cpt2.phage.intron_detection", - "gff3.rebase", - "edu.tamu.cpt.gff3.intersect_and_adjacent", + "edu.tamu.cpt.gff3.require_phage_start", + "get_orfs_or_cdss", "edu.tamu.cpt.gff3.export_seq", + "edu.tamu.cpt2.phage.intron_detection", + "edu.tamu.cpt.gff3.remove_annots", + "ncbi_blastp_wrapper", "edu.tamu.cpt.fasta.seq_trans", - "edu.tamu.cpt.gff3.cdsParents", - "edu.tamu.cpt2.gff3.splitGff" + "edu.tamu.cpt.gff3.intersect_and_adjacent", + "edu.tamu.cpt2.gff3.splitGff", + "fetch_jbrowse", + "gff3.rebase", + "interproscan", + "jbrowse" ], "update_time": "2024-10-28", "versions": 30 @@ -18808,8 +34015,8 @@ "doi": "", "edam_operation": [ "Pairwise sequence alignment", - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "c879060c00aab94f", @@ -18822,8 +34029,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "freebayes", - "minimap2" + "minimap2", + "freebayes" ], "update_time": "2024-10-26", "versions": 14 @@ -18833,20 +34040,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Coding region prediction", - "De-novo assembly", + "Gene prediction", + "Genome annotation", + "Sequence clustering", + "Visualisation", + "Phylogenetic tree generation", "Differential gene expression analysis", + "Sequence alignment", "Formatting", + "Coding region prediction", + "De-novo assembly", "Variant calling", - "Phylogenetic tree generation", - "Sequence alignment", "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Gene prediction", - "Genome annotation", - "Sequence clustering", - "Phylogenetic tree visualisation" + "Phylogenetic tree visualisation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "6d87481be47902e1", @@ -18859,16 +34066,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "velveth", - "abricate", + "prokka", "trimmomatic", - "snippy", - "quast", - "fastq_paired_end_interlacer", - "velvetg", + "abricate", "antismash", + "velvetg", + "fastq_paired_end_interlacer", + "velveth", + "quast", + "snippy", "hisat2", - "prokka", "staramr_search" ], "update_time": "2024-10-25", @@ -18880,10 +34087,10 @@ "doi": "", "edam_operation": [ "Genome annotation", - "Sequence assembly", + "Read binning", "Sequence clustering", - "Read mapping", - "Read binning" + "Sequence assembly", + "Read mapping" ], "edam_topic": [], "id": "43098b8afe78b071", @@ -18896,28 +34103,28 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "concoct_extract_fasta_bins", - "Fasta_to_Contig2Bin", + "cami_amber", + "concoct_cut_up_fasta", + "bowtie2", + "collection_element_identifiers", + "param_value_from_file", "samtools_sort", - "split_file_to_collection", "concoct_merge_cut_up_clustering", - "concoct", - "metabat2", "semibin", "cami_amber_add", - "param_value_from_file", - "metabat2_jgi_summarize_bam_contig_depths", - "cat_multi_datasets", + "concoct_extract_fasta_bins", + "metabat2", "compose_text_param", - "cami_amber", - "__RELABEL_FROM_FILE__", + "concoct", "tp_replace_in_column", + "__RELABEL_FROM_FILE__", + "metabat2_jgi_summarize_bam_contig_depths", + "Fasta_to_Contig2Bin", + "split_file_to_collection", + "cat_multi_datasets", "das_tool", "concoct_coverage_table", - "tp_awk_tool", - "collection_element_identifiers", - "concoct_cut_up_fasta", - "bowtie2" + "tp_awk_tool" ], "update_time": "2024-10-25", "versions": 3 @@ -18931,12 +34138,12 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", "Sequence contamination filtering", - "Read pre-processing", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Nucleic acid design", + "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", "Validation" ], @@ -18952,20 +34159,21 @@ "tags": [ "mgnify_amplicon", "amplicon", - "metagenomics" + "metagenomics", + "name:microgalaxy" ], "tools": [ - "prinseq", + "fastq_filter", + "fastq_to_fasta_python", "trimmomatic", - "mgnify_seqprep", "tp_find_and_replace", - "__UNZIP_COLLECTION__", + "prinseq", + "mgnify_seqprep", "fastp", - "fastq_filter", - "cshl_fasta_formatter", "multiqc", + "cshl_fasta_formatter", "fastqc", - "fastq_to_fasta_python" + "__UNZIP_COLLECTION__" ], "update_time": "2024-10-25", "versions": 16 @@ -18979,13 +34187,13 @@ ], "doi": "", "edam_operation": [ + "k-mer counting", + "Mapping", "Visualisation", - "Comparison", "Alignment", "Nucleic acid feature detection", - "Mapping", "Formatting", - "k-mer counting" + "Comparison" ], "edam_topic": [], "id": "0c3eee883f5ab977", @@ -18999,22 +34207,23 @@ "tags": [ "mgnify_amplicon", "metagenomics", - "amplicon" + "amplicon", + "name:microgalaxy" ], "tools": [ - "infernal_cmsearch", - "gops_concat_1", - "tp_awk_tool", "collection_element_identifiers", + "gops_concat_1", + "infernal_cmsearch", + "taxonomy_krona_chart", + "cmsearch_deoverlap", + "cshl_fasta_formatter", "__FILTER_EMPTY_DATASETS__", - "__FILTER_FROM_FILE__", - "mapseq", - "bedtools_getfastabed", "biom_convert", - "taxonomy_krona_chart", + "mapseq", "query_tabular", - "cshl_fasta_formatter", - "cmsearch_deoverlap" + "bedtools_getfastabed", + "__FILTER_FROM_FILE__", + "tp_awk_tool" ], "update_time": "2024-10-25", "versions": 31 @@ -19038,14 +34247,15 @@ "tags": [ "mgnify_amplicon", "amplicon", - "metagenomics" + "metagenomics", + "name:microgalaxy" ], "tools": [ - "tp_awk_tool", "filter_tabular", + "map_param_value", "Grouping1", "collection_column_join", - "map_param_value" + "tp_awk_tool" ], "update_time": "2024-10-25", "versions": 1 @@ -19059,10 +34269,10 @@ ], "doi": "", "edam_operation": [ - "Mapping", + "k-mer counting", "Visualisation", "Formatting", - "k-mer counting" + "Mapping" ], "edam_topic": [], "id": "169327ba670607d1", @@ -19076,17 +34286,18 @@ "tags": [ "mgnify_amplicon", "amplicon", - "metagenomics" + "metagenomics", + "name:microgalaxy" ], "tools": [ - "bedtools_maskfastabed", "collection_element_identifiers", + "taxonomy_krona_chart", "__FILTER_EMPTY_DATASETS__", - "__FILTER_FROM_FILE__", - "mapseq", - "tp_awk_tool", + "bedtools_maskfastabed", "biom_convert", - "taxonomy_krona_chart" + "mapseq", + "__FILTER_FROM_FILE__", + "tp_awk_tool" ], "update_time": "2024-10-25", "versions": 24 @@ -19110,14 +34321,15 @@ "tags": [ "mgnify_amplicon", "amplicon", - "metagenomics" + "metagenomics", + "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "query_tabular", - "Grouping1", + "filter_tabular", "collection_column_join", - "filter_tabular" + "Grouping1", + "query_tabular", + "tp_awk_tool" ], "update_time": "2024-10-25", "versions": 69 @@ -19154,13 +34366,13 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "26185e8fa5a9b988", @@ -19178,13 +34390,13 @@ "features" ], "tools": [ - "fastqc", - "trimmomatic", - "umi_tools_dedup", "featurecounts", - "hisat2", + "trimmomatic", "multiqc", - "umi_tools_extract" + "umi_tools_extract", + "umi_tools_dedup", + "fastqc", + "hisat2" ], "update_time": "2024-10-22", "versions": 13 @@ -19194,8 +34406,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "41d096891bada138", @@ -19210,14 +34422,14 @@ "tools": [ "cat1", "FileConverter", - "search_gui", - "peptide_shaker", + "query_tabular", "tab2fasta", + "PeakPickerHiRes", + "search_gui", "ident_params", - "query_tabular", - "dbbuilder", "mz_to_sqlite", - "PeakPickerHiRes" + "dbbuilder", + "peptide_shaker" ], "update_time": "2024-10-21", "versions": 0 @@ -19240,11 +34452,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-10-19", "versions": 0 @@ -19254,15 +34466,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Mapping", "Sequence assembly", "Formatting", - "Data retrieval", "Query and retrieval", - "Taxonomic classification", - "Mapping", + "Generation", + "Data retrieval", "Genome alignment", - "Generation" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "e4dabaf57668dbd1", @@ -19276,14 +34488,14 @@ "tags": [], "tools": [ "gtdb_to_taxdump", - "Cut1", - "cat_multi_datasets", "compose_text_param", + "gtdbtk_classify_wf", "biobox_add_taxid", + "cat_multi_datasets", "cami_amber_convert", "tp_replace_in_column", "name2taxid", - "gtdbtk_classify_wf" + "Cut1" ], "update_time": "2024-10-18", "versions": 1 @@ -19311,8 +34523,8 @@ ], "tools": [ "tp_cut_tool", - "obisindicators", - "obis_data" + "obis_data", + "obisindicators" ], "update_time": "2024-10-18", "versions": 8 @@ -19338,9 +34550,9 @@ "ocean" ], "tools": [ + "interactive_tool_divand", "interactive_tool_odv", - "divand_full_analysis", - "interactive_tool_divand" + "divand_full_analysis" ], "update_time": "2024-10-17", "versions": 18 @@ -19350,11 +34562,11 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence composition calculation", "Visualisation", "Statistical calculation", - "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "95cb04ffb473623b", @@ -19367,11 +34579,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", - "tp_sorted_uniq", - "fastq_paired_end_interlacer", "multiqc", - "fastqc" + "fastq_paired_end_interlacer", + "ggplot2_point", + "fastqc", + "tp_sorted_uniq" ], "update_time": "2024-10-17", "versions": 0 @@ -19383,11 +34595,11 @@ ], "doi": "", "edam_operation": [ + "Transcriptome assembly", + "Annotation", "Classification", "Sequence annotation", - "RNA-Seq analysis", - "Annotation", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "93e576fca98a554d", @@ -19400,10 +34612,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gffread", - "feelnc", + "cat1", "stringtie", - "cat1" + "gffread", + "feelnc" ], "update_time": "2024-10-17", "versions": 9 @@ -19413,18 +34625,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Editing", - "Sequence annotation", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", + "Editing", + "Scaffolding", "Differential protein expression profiling", - "RNA-Seq analysis", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "7de6e20699183cd3", @@ -19444,12 +34656,12 @@ "tools": [ "jcvi_gff_stats", "gffread", - "omark", + "compleasm", "helixer", "red", - "compleasm", "busco", - "jbrowse" + "jbrowse", + "omark" ], "update_time": "2024-10-17", "versions": 4 @@ -19464,16 +34676,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "dfb8e0f3c534000e", @@ -19493,12 +34705,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-17", "versions": 1 @@ -19513,16 +34725,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "a18aed4b03ffd27e", @@ -19542,12 +34754,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-17", "versions": 1 @@ -19575,9 +34787,9 @@ "tags": [], "tools": [ "map_param_value", - "brew3r_r", "stringtie", - "stringtie_merge" + "stringtie_merge", + "brew3r_r" ], "update_time": "2024-10-17", "versions": 1 @@ -19592,14 +34804,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "47e14222073e7192", @@ -19621,12 +34833,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-17", "versions": 1 @@ -19641,14 +34853,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "ebb131f2a6172081", @@ -19670,12 +34882,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-17", "versions": 1 @@ -19690,12 +34902,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "b93333efdab316d8", @@ -19716,13 +34928,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-10-17", "versions": 1 @@ -19738,8 +34950,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "34df701aa23a9fb3", @@ -19763,10 +34975,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-17", "versions": 1 @@ -19782,8 +34994,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "1ce523ef51f47134", @@ -19807,10 +35019,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-17", "versions": 1 @@ -19822,13 +35034,13 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "2179ba1c33f77f7e", @@ -19848,13 +35060,13 @@ "metams" ], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "checkFormat", "xcms_plot_chromatogram", - "Multivariate" + "msnbase_readmsdata", + "checkFormat", + "Multivariate", + "xcms_merge" ], "update_time": "2024-10-17", "versions": 1 @@ -19864,10 +35076,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Visualisation", + "Standardisation and normalisation", "Statistical calculation", - "Standardisation and normalisation" + "Filtering", + "Visualisation" ], "edam_topic": [], "id": "e1296dbcf34499b0", @@ -19890,16 +35102,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "865f470be3c18b08", @@ -19912,15 +35124,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2024-10-13", "versions": 6 @@ -19930,16 +35142,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f560e06d23818b4c", @@ -19952,15 +35164,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", + "trimmomatic", "CONVERTER_Bam_Bai_0", + "vcffilter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2024-10-13", "versions": 1 @@ -19970,16 +35182,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ea0524e0b5eab8b9", @@ -19992,15 +35204,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2024-10-12", "versions": 1 @@ -20010,16 +35222,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "3b7c0b64033f38ac", @@ -20032,15 +35244,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2024-10-11", "versions": 0 @@ -20050,14 +35262,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", "De-novo assembly", - "Sequencing quality control", "Genome assembly", "Multilocus sequence typing", - "Taxonomic classification", "Mapping assembly", - "Cross-assembly" + "Sequencing quality control", + "Filtering", + "Cross-assembly", + "Taxonomic classification" ], "edam_topic": [], "id": "201e65bcf2b71584", @@ -20070,14 +35282,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "kraken2", "flye", + "fastq_to_fasta_python", + "kraken2", "porechop", + "kraken-report", "filtlong", "mlst", - "kraken-report", - "staramr_search", - "fastq_to_fasta_python" + "staramr_search" ], "update_time": "2024-10-10", "versions": 8 @@ -20100,12 +35312,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "CONVERTER_interval_to_bedstrict_0", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "CONVERTER_interval_to_bedstrict_0", + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-10-08", "versions": 1 @@ -20126,14 +35338,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "table_compute", "seurat_reduce_dimension", + "seurat_clustering", "seurat_preprocessing", + "table_compute", "seurat_plot", - "csv_to_tabular", + "seurat_create", "seurat_data", - "seurat_clustering", - "seurat_create" + "csv_to_tabular" ], "update_time": "2024-10-08", "versions": 3 @@ -20143,11 +35355,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Phylogenetic tree generation", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "dc57118a95b10a80", @@ -20160,9 +35372,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "newick_display", "muscle", - "fasttree", - "newick_display" + "fasttree" ], "update_time": "2024-10-07", "versions": 1 @@ -20185,11 +35397,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-10-07", "versions": 1 @@ -20220,16 +35432,16 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", + "datamash_ops", "anndata_import", "scanpy_plot", + "anndata_manipulate", "scanpy_inspect", - "scanpy_filter", "scanpy_normalize", + "scanpy_remove_confounders", "scanpy_cluster_reduce_dimension", - "datamash_ops", - "scanpy_remove_confounders" + "scanpy_filter", + "anndata_inspect" ], "update_time": "2024-10-04", "versions": 5 @@ -20245,8 +35457,8 @@ "doi": "", "edam_operation": [ "Genome visualisation", - "Pathway visualisation", - "Structure visualisation" + "Structure visualisation", + "Pathway visualisation" ], "edam_topic": [], "id": "972db4abc51bb3ab", @@ -20259,12 +35471,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", + "jbrowse2", "filter_by_fasta_ids", + "tp_easyjoin_tool", "Cut1", - "fasta_compute_length", - "jbrowse2" + "fasta_compute_length" ], "update_time": "2024-10-04", "versions": 123 @@ -20316,14 +35528,14 @@ "name:single-cell" ], "tools": [ - "snapatac2_plotting", + "collection_element_identifiers", "__EXTRACT_DATASET__", + "Show beginning1", + "snapatac2_plotting", "anndata_manipulate", - "collection_element_identifiers", - "__FILTER_FROM_FILE__", + "snapatac2_preprocessing", "snapatac2_clustering", - "Show beginning1", - "snapatac2_preprocessing" + "__FILTER_FROM_FILE__" ], "update_time": "2024-10-03", "versions": 30 @@ -20335,14 +35547,14 @@ ], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "0135ee4b3fa0cbce", @@ -20357,8 +35569,8 @@ "name:clinicalmp" ], "tools": [ - "Cut1", "Grep1", + "Cut1", "Grouping1", "maxquant" ], @@ -20386,20 +35598,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-10-03", "versions": 1 @@ -20411,14 +35623,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "52bdf400f97c5770", @@ -20435,26 +35647,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-10-03", "versions": 1 @@ -20466,11 +35678,11 @@ ], "doi": "", "edam_operation": [ - "Genome visualisation", - "Structural variation detection", + "Pairwise sequence alignment", "Sequence analysis", "Pathway visualisation", - "Pairwise sequence alignment", + "Structural variation detection", + "Genome visualisation", "Structure visualisation" ], "edam_topic": [], @@ -20484,21 +35696,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", "Add_a_column1", "deeptools_bam_coverage", + "tp_replace_in_line", + "deeptools_bigwig_compare", + "deeptools_bam_compare", + "samtools_view", + "jbrowse2", "filter_by_fasta_ids", + "tp_easyjoin_tool", + "minimap2", "Cut1", - "samtools_view", - "tp_replace_in_line", "pick_value", "sniffles", - "minimap2", - "deeptools_bigwig_compare", - "deeptools_bam_compare", - "fasta_compute_length", - "jbrowse2" + "fasta_compute_length" ], "update_time": "2024-10-02", "versions": 201 @@ -20522,8 +35734,8 @@ "ospd" ], "tools": [ - "psy_maps", - "c3s" + "c3s", + "psy_maps" ], "update_time": "2024-10-02", "versions": 18 @@ -20538,13 +35750,13 @@ ], "doi": "", "edam_operation": [ - "Data handling", "Genome annotation", - "Sequence file editing", - "Structural variation detection", - "Mapping", + "Pairwise sequence alignment", "Sequence analysis", - "Pairwise sequence alignment" + "Data handling", + "Structural variation detection", + "Sequence file editing", + "Mapping" ], "edam_topic": [], "id": "2880a32a52d27743", @@ -20557,19 +35769,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "bbgtobigwig", + "seqtk_telo", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", + "gfastats", + "repeatmasker_wrapper", + "bedtools_makewindowsbed", "windowmasker_mkcounts", - "seqtk_telo", + "bbgtobigwig", + "minimap2", "pick_value", "sniffles", - "minimap2", - "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", - "gfastats" + "fasta_compute_length" ], "update_time": "2024-10-02", "versions": 41 @@ -20579,16 +35791,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "f21d6a40a10a8ae8", @@ -20603,39 +35815,39 @@ "microbiome" ], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_cluster", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_seq_error", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", "mothur_remove_groups", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", + "mothur_pre_cluster", "mothur_get_groups", - "mothur_align_seqs", + "mothur_chimera_vsearch", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_cluster", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", - "XY_Plot_1", - "mothur_seq_error" + "XY_Plot_1" ], "update_time": "2024-10-01", "versions": 1 @@ -20648,26 +35860,26 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequence assembly", - "Sequencing quality control", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", "Visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", + "Sequence assembly", "Mapping assembly", "Parsing", + "Sequencing quality control", + "Base-calling", "Cross-assembly", - "Filtering", + "Box-Whisker plot plotting", + "Sequence assembly validation", + "Statistical calculation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", + "Multilocus sequence typing", + "De-novo assembly", "Sequence composition calculation", + "Antimicrobial resistance prediction", "Variant calling", - "Multilocus sequence typing", - "Sequence assembly validation", - "Statistical calculation", - "Base-calling" + "Filtering", + "Data handling" ], "edam_topic": [], "id": "eb5ab8bc82569eee", @@ -20680,22 +35892,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "hamronize_tool", - "abricate", "flye", - "filtlong", - "mlst", - "bandage_image", + "bandage_info", + "abritamr", + "hamronize_summarize", + "ncbi_blastn_wrapper", + "abricate", "nanoplot", + "bandage_image", "quast", - "abritamr", "medaka_consensus_pipeline", - "amrfinderplus", - "hamronize_summarize", "fastqc", - "ncbi_blastn_wrapper", + "amrfinderplus", + "filtlong", + "mlst", "staramr_search", - "bandage_info" + "hamronize_tool" ], "update_time": "2024-10-01", "versions": 13 @@ -20705,19 +35917,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence annotation", - "Sequencing quality control", - "Phylogenetic analysis", - "Formatting", "Visualisation", "Sequence clustering", - "Sequence file editing", - "DNA barcoding", "Sequence alignment", + "DNA barcoding", + "Sequencing quality control", + "Sequence annotation", + "Phylogenetic analysis", "Demultiplexing", - "Taxonomic classification", - "Sequence read processing" + "Sequence file editing", + "Formatting", + "Sequence read processing", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "8f747dbff3216993", @@ -20730,22 +35942,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ncbi_blastx_wrapper", - "blastxml_to_top_descr", + "qiime_make_otu_table", "mothur_screen_seqs", - "cshl_fastx_trimmer", - "biopython_base_distribution", - "mothur_remove_seqs", + "qiime_pick_rep_set", "seqtk_sample", - "qiime_pick_otus", - "mothur_chimera_vsearch", "biom_summarize_table", + "ncbi_blastx_wrapper", "ncbi_tblastx_wrapper", "blastxml_to_tabular", - "tp_text_file_with_recurring_lines", - "qiime_make_otu_table", + "mothur_chimera_vsearch", + "biopython_base_distribution", + "mothur_remove_seqs", "mothur_make_contigs", - "qiime_pick_rep_set" + "tp_text_file_with_recurring_lines", + "blastxml_to_top_descr", + "cshl_fastx_trimmer", + "qiime_pick_otus" ], "update_time": "2024-10-01", "versions": 23 @@ -20755,19 +35967,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence annotation", - "Sequencing quality control", - "Phylogenetic analysis", - "Formatting", "Visualisation", "Sequence clustering", - "Sequence file editing", - "DNA barcoding", "Sequence alignment", + "DNA barcoding", + "Sequencing quality control", + "Sequence annotation", + "Phylogenetic analysis", "Demultiplexing", - "Taxonomic classification", - "Sequence read processing" + "Sequence file editing", + "Formatting", + "Sequence read processing", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "e14b81a8c0b1b7a4", @@ -20780,20 +35992,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ncbi_blastx_wrapper", - "blastxml_to_top_descr", + "qiime_make_otu_table", "mothur_screen_seqs", - "cshl_fastx_trimmer", - "biopython_base_distribution", + "qiime_pick_rep_set", "seqtk_sample", - "qiime_pick_otus", "biom_summarize_table", + "ncbi_blastx_wrapper", "ncbi_tblastx_wrapper", "blastxml_to_tabular", - "tp_text_file_with_recurring_lines", - "qiime_make_otu_table", + "biopython_base_distribution", "mothur_make_contigs", - "qiime_pick_rep_set" + "tp_text_file_with_recurring_lines", + "blastxml_to_top_descr", + "cshl_fastx_trimmer", + "qiime_pick_otus" ], "update_time": "2024-10-01", "versions": 52 @@ -20803,14 +36015,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Rarefaction", + "Pathway analysis", + "Visualisation", "Expression analysis", - "Phylogenetic reconstruction", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Pathway analysis", - "Visualisation", + "Rarefaction", + "Phylogenetic reconstruction", "Taxonomic classification" ], "edam_topic": [], @@ -20824,15 +36036,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "qiime2__taxa__collapse", - "picrust2_pipeline", - "qiime2_core__tools__import", - "qiime2__dada2__denoise_paired", - "qiime2__demux__summarize", + "qiime_extract_viz", "qiime2__feature_classifier__classify_sklearn", + "qiime2__dada2__denoise_paired", + "picrust2_pipeline", "qiime2__feature_table__relative_frequency", - "qiime2_core__tools__export", - "qiime_extract_viz" + "qiime2__demux__summarize", + "qiime2_core__tools__import", + "qiime2__taxa__collapse", + "qiime2_core__tools__export" ], "update_time": "2024-09-26", "versions": 8 @@ -20844,10 +36056,10 @@ ], "doi": "", "edam_operation": [ - "Sequence annotation", "Visualisation", + "Sequence clustering", "Sequence cluster visualisation", - "Sequence clustering" + "Sequence annotation" ], "edam_topic": [], "id": "86465932556bc96c", @@ -20866,13 +36078,13 @@ "virus" ], "tools": [ - "virannot_blast2tsv", - "virAnnot_rps2tsv", - "taxonomy_krona_chart", + "ncbi_tblastx_wrapper", "virannot_otu", + "taxonomy_krona_chart", + "virannot_blast2tsv", + "krona-text", "ncbi_rpstblastn_wrapper", - "ncbi_tblastx_wrapper", - "krona-text" + "virAnnot_rps2tsv" ], "update_time": "2024-09-26", "versions": 6 @@ -20887,16 +36099,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "d8db0b2e30370b84", @@ -20916,12 +36128,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-26", "versions": 1 @@ -20936,12 +36148,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "723e718f37e9ab91", @@ -20962,13 +36174,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-26", "versions": 1 @@ -20984,8 +36196,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "e37cc0b64774561b", @@ -21009,10 +36221,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-26", "versions": 1 @@ -21028,11 +36240,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "a3cb75fd31ba0689", @@ -21080,9 +36292,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-26", "versions": 1 @@ -21111,14 +36323,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-26", "versions": 1 @@ -21146,17 +36358,17 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", - "gfastats", - "Cut1", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_sed_tool", "tp_grep_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "tp_cat", + "gfastats", + "tp_sed_tool", + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-26", "versions": 1 @@ -21184,15 +36396,15 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", + "ncbi_blastn_wrapper", + "tp_cat", "gfastats", - "Cut1", "tp_sed_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-26", "versions": 1 @@ -21206,10 +36418,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "020f877513f2d0d1", @@ -21224,24 +36436,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -21255,10 +36467,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "117177b0c231dc55", @@ -21273,23 +36485,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -21303,10 +36515,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0ae360bfbb3b2494", @@ -21321,23 +36533,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -21349,14 +36561,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d6809603f46de1b3", @@ -21371,14 +36583,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -21390,14 +36602,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "409336bf210033a2", @@ -21412,14 +36624,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -21431,15 +36643,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a76629eccfdeafb8", @@ -21454,13 +36666,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -21472,19 +36684,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "30e7dc81e323cbdb", @@ -21499,27 +36711,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -21531,15 +36743,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b5e3360f933d1950", @@ -21554,13 +36766,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -21572,17 +36784,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "478190607a114390", @@ -21597,15 +36809,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-26", "versions": 1 @@ -21626,8 +36838,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Show beginning1", - "hirondelle_crim" + "hirondelle_crim", + "Show beginning1" ], "update_time": "2024-09-25", "versions": 10 @@ -21637,14 +36849,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Phylogenetic tree analysis", "Visualisation", + "Nucleic acid sequence analysis", + "Phylogenetic tree editing", + "Phylogenetic tree analysis", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Nucleic acid sequence analysis", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "79b4ae4403772098", @@ -21657,12 +36869,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metaphlan", + "export2graphlan", "graphlan_annotate", - "Cut1", - "graphlan", "taxonomy_krona_chart", - "export2graphlan" + "graphlan", + "metaphlan", + "Cut1" ], "update_time": "2024-09-23", "versions": 0 @@ -21672,25 +36884,25 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", + "Genome annotation", + "Sequence contamination filtering", + "Visualisation", + "Sequence alignment", "Sequence assembly", "Sequencing quality control", - "Sequence assembly visualisation", - "Visualisation", - "Sequence contamination filtering", - "Genome assembly", - "Genome indexing", - "Generation", - "Optimisation and refinement", "Aggregation", - "Read mapping", - "Sequence alignment", + "Coding region prediction", "Sequence assembly validation", + "Read mapping", "Gene prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction" + "Genome assembly", + "Sequence assembly visualisation", + "Optimisation and refinement", + "Generation", + "Genome indexing", + "Sequence alignment analysis", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "98bfad0c684011e9", @@ -21708,27 +36920,27 @@ "dnaseq" ], "tools": [ - "samtools_view", - "bandage_image", "krakentools_extract_kraken_reads", - "__UNZIP_COLLECTION__", - "fastp", - "bamtools_split_ref", - "ivar_consensus", - "megahit", - "prokka", - "fasta_filter_by_length", - "spades", "collapse_dataset", - "samtools_fastx", - "quast", - "qualimap_bamqc", "regex_replace", + "tp_cat", + "qualimap_bamqc", + "prokka", + "quast", "bwa_mem", + "bamtools_split_ref", + "samtools_view", + "__UNZIP_COLLECTION__", "kraken2", + "samtools_fastx", + "ivar_consensus", + "megahit", + "bandage_image", "velvetoptimiser", "cap3", - "tp_cat" + "fasta_filter_by_length", + "spades", + "fastp" ], "update_time": "2024-09-23", "versions": 56 @@ -21751,9 +36963,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bigwig_outlier_bed", "microsatbed", - "pick_value" + "pick_value", + "bigwig_outlier_bed" ], "update_time": "2024-09-22", "versions": 36 @@ -21784,27 +36996,27 @@ "name:public-data" ], "tools": [ - "anndata_ops", - "scanpy_read_10x", - "tp_grep_tool", - "scanpy_run_umap", + "scanpy_plot", + "scanpy_find_markers", "scanpy_filter_genes", - "scanpy_find_variable_genes", - "datamash_transpose", "join1", + "tp_grep_tool", + "scanpy_normalise_data", "scanpy_compute_graph", - "scanpy_plot_embed", - "scanpy_run_tsne", - "scanpy_find_markers", - "scanpy_find_cluster", - "scanpy_scale_data", - "scanpy_run_pca", + "regexColumn1", "retrieve_scxa", + "scanpy_find_variable_genes", + "scanpy_filter_cells", + "scanpy_run_umap", "anndata_inspect", - "scanpy_plot", - "regexColumn1", - "scanpy_normalise_data", - "scanpy_filter_cells" + "scanpy_run_tsne", + "scanpy_run_pca", + "scanpy_find_cluster", + "datamash_transpose", + "scanpy_read_10x", + "anndata_ops", + "scanpy_plot_embed", + "scanpy_scale_data" ], "update_time": "2024-09-20", "versions": 2 @@ -21817,10 +37029,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -21835,10 +37047,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-09-19", "versions": 1 @@ -21874,9 +37086,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "ad8b6d73c9654305", @@ -21894,8 +37106,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-09-19", @@ -21912,12 +37124,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "f6a763951d815944", @@ -21935,28 +37147,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-09-19", "versions": 1 @@ -21970,19 +37182,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "344cd3a3c2ce5302", @@ -22001,23 +37213,23 @@ "name:iwc" ], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -22031,15 +37243,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "77e5bbd317750915", @@ -22057,18 +37269,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-09-19", "versions": 1 @@ -22101,24 +37313,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -22151,24 +37363,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -22181,8 +37393,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "389d992ff7268247", @@ -22195,18 +37407,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -22219,8 +37431,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "9aa290ce1927d700", @@ -22233,18 +37445,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -22259,16 +37471,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "61948fcaefa1418a", @@ -22288,12 +37500,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-19", "versions": 1 @@ -22308,16 +37520,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "8792eaecb69fbc26", @@ -22337,12 +37549,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-19", "versions": 1 @@ -22357,16 +37569,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "36ea584e0f60893e", @@ -22386,12 +37598,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-19", "versions": 1 @@ -22406,16 +37618,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "bcd50e655809cfcb", @@ -22435,12 +37647,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-19", "versions": 1 @@ -22455,16 +37667,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "4a218fb93d78ba67", @@ -22484,12 +37696,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-19", "versions": 1 @@ -22517,9 +37729,9 @@ "tags": [], "tools": [ "map_param_value", - "brew3r_r", "stringtie", - "stringtie_merge" + "stringtie_merge", + "brew3r_r" ], "update_time": "2024-09-19", "versions": 1 @@ -22534,14 +37746,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "884a4415b669690c", @@ -22563,12 +37775,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-09-19", "versions": 1 @@ -22583,14 +37795,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "aafcfcb585c5ca75", @@ -22612,12 +37824,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-09-19", "versions": 1 @@ -22632,14 +37844,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "0c47571d20535426", @@ -22661,12 +37873,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-09-19", "versions": 1 @@ -22681,14 +37893,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "0a82eb8b44d9d502", @@ -22710,12 +37922,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-09-19", "versions": 1 @@ -22730,12 +37942,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "3d937648809ca4e7", @@ -22756,13 +37968,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -22777,12 +37989,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "fca458178b3c794a", @@ -22803,13 +38015,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -22824,12 +38036,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "4216424f032c055f", @@ -22850,13 +38062,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -22872,8 +38084,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "41d207d06a32ba05", @@ -22897,10 +38109,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-19", "versions": 1 @@ -22916,8 +38128,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "abe85758e77c78e6", @@ -22941,10 +38153,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-19", "versions": 1 @@ -22960,8 +38172,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "f30f8e7dcd50cd0d", @@ -22985,10 +38197,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-19", "versions": 1 @@ -23001,10 +38213,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23019,8 +38231,8 @@ "tags": [], "tools": [ "qiime2__metadata__tabulate", - "qiime2__dada2__denoise_paired", "qiime2__feature_table__tabulate_seqs", + "qiime2__dada2__denoise_paired", "qiime2__feature_table__summarize" ], "update_time": "2024-09-19", @@ -23034,10 +38246,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23067,10 +38279,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23086,8 +38298,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -23101,10 +38313,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23120,8 +38332,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -23135,10 +38347,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23153,8 +38365,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_paired", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -23167,10 +38379,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -23185,8 +38397,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -23199,8 +38411,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "642f4c47028031d7", @@ -23215,17 +38427,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-09-19", "versions": 1 @@ -23238,16 +38450,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "5bf6718e7d6158d2", @@ -23262,17 +38474,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23285,16 +38497,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "032a7281a86eba0d", @@ -23309,17 +38521,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23332,16 +38544,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d02458f1d7d9c3f4", @@ -23356,20 +38568,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23382,16 +38594,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "aef62f4d0bba003b", @@ -23406,20 +38618,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23434,10 +38646,10 @@ ], "doi": "", "edam_operation": [ - "Mapping", - "Protein sequence analysis", "Pairwise sequence alignment", - "Sequence alignment" + "Protein sequence analysis", + "Sequence alignment", + "Mapping" ], "edam_topic": [], "id": "0c92c3c322c3effe", @@ -23450,9 +38662,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bedtools_bamtobed", "minimap2", "miniprot", - "bedtools_bamtobed", "pick_value" ], "update_time": "2024-09-19", @@ -23467,20 +38679,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fb015e398373ea8a", @@ -23496,23 +38708,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23526,20 +38738,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "b4948afacccfefdb", @@ -23555,23 +38767,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23585,20 +38797,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "847403b72dd346ff", @@ -23614,23 +38826,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23644,20 +38856,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3a3e2d50fe7a9ee3", @@ -23673,26 +38885,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23706,20 +38918,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "4856e3522b2ee059", @@ -23735,26 +38947,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23768,20 +38980,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3eb6663a66f8e69a", @@ -23797,26 +39009,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23829,20 +39041,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f1ca4289ee4f67bb", @@ -23858,22 +39070,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23886,20 +39098,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e8f9e1d911683b22", @@ -23915,22 +39127,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -23943,20 +39155,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1ac0a15758277730", @@ -23972,22 +39184,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24000,20 +39212,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "c508c00e81018dd8", @@ -24029,22 +39241,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24057,20 +39269,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e7aebe58411d97ed", @@ -24086,25 +39298,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24117,8 +39329,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "319bc351f7a8e358", @@ -24133,11 +39345,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -24150,8 +39362,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "f6bd10486a0ba17d", @@ -24166,12 +39378,12 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", - "tp_find_and_replace", "param_value_from_file", - "gfastats" + "tp_find_and_replace", + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -24198,8 +39410,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -24226,8 +39438,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -24254,8 +39466,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -24268,16 +39480,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "b5de94e9cde071ab", @@ -24293,16 +39505,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24315,16 +39527,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "6c14b08a7ef7e79a", @@ -24340,16 +39552,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24362,16 +39574,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0a3ebee985c26060", @@ -24387,20 +39599,20 @@ ], "tools": [ "cat1", + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "merqury", "gfastats", - "Cut1", - "tp_awk_tool", + "busco", "join1", - "param_value_from_file", "tp_cut_tool", - "tp_find_and_replace", "minimap2", - "merqury", - "compose_text_param", - "busco", - "purge_dups" + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24413,13 +39625,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24435,19 +39647,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24460,13 +39672,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24482,19 +39694,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24507,13 +39719,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24529,20 +39741,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24555,13 +39767,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24577,20 +39789,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24603,13 +39815,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24625,20 +39837,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24651,13 +39863,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -24673,21 +39885,21 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "compose_text_param", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -24700,8 +39912,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "7341ca7572447d60", @@ -24714,8 +39926,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -24728,8 +39940,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "49d913cefc5daaf3", @@ -24756,19 +39968,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "023a0ee62dd1f593", @@ -24784,21 +39996,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24811,19 +40023,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e935d2c8ffb52588", @@ -24839,21 +40051,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24866,19 +40078,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "bef0a7d604f2ebef", @@ -24894,21 +40106,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24921,19 +40133,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "57cc33ed64d71982", @@ -24949,21 +40161,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -24976,19 +40188,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "b8baade87e733fce", @@ -25004,21 +40216,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25031,20 +40243,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "089e5e83b1de0511", @@ -25060,25 +40272,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25091,20 +40303,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "bcf99cc0469db276", @@ -25120,25 +40332,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25161,14 +40373,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2024-09-19", "versions": 1 @@ -25182,10 +40394,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2f094f5e1f391529", @@ -25200,24 +40412,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25231,10 +40443,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a639ea0419de1078", @@ -25249,24 +40461,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25280,10 +40492,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5cc732a6b4338bf5", @@ -25298,23 +40510,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25328,10 +40540,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "079e2a968d8e6176", @@ -25346,23 +40558,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25376,10 +40588,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1c267e93aa8015e6", @@ -25394,23 +40606,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25424,10 +40636,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b57c3522bdd7c2d5", @@ -25442,23 +40654,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -25471,17 +40683,17 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Local alignment", - "Sequence alignment", + "Generation", "Genome indexing", - "Sequence contamination filtering", - "Global alignment", + "Sequence alignment analysis", "Sequence analysis", - "Generation", - "Validation" + "Global alignment", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "6e1fe7372e93fae0", @@ -25497,31 +40709,31 @@ "virology" ], "tools": [ - "samtools_view", - "fastp", "samtools_merge", - "ivar_consensus", - "split_file_to_collection", - "tp_sed_tool", - "EMBOSS: maskseq51", - "datamash_ops", - "samtools_stats", - "__ZIP_COLLECTION__", - "__FILTER_FAILED_DATASETS__", - "param_value_from_file", - "compose_text_param", - "__SORTLIST__", + "Cut1", + "tp_cat", + "Grep1", "__APPLY_RULES__", "qualimap_bamqc", - "__FLATTEN__", - "fasta_compute_length", - "ivar_trim", - "bwa_mem", "collection_element_identifiers", - "Cut1", + "param_value_from_file", + "EMBOSS: maskseq51", "multiqc", - "Grep1", - "tp_cat" + "__SORTLIST__", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "fasta_compute_length", + "compose_text_param", + "ivar_consensus", + "__ZIP_COLLECTION__", + "samtools_stats", + "fastp", + "__FILTER_FAILED_DATASETS__", + "split_file_to_collection", + "tp_sed_tool", + "datamash_ops" ], "update_time": "2024-09-19", "versions": 1 @@ -25546,9 +40758,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2024-09-19", "versions": 1 @@ -25577,8 +40789,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2024-09-19", @@ -25620,14 +40832,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ead0f264798f9418", @@ -25642,14 +40854,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25661,14 +40873,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9da26c5131603b9f", @@ -25683,14 +40895,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25702,14 +40914,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "c4fa05e209a2f082", @@ -25724,14 +40936,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25743,14 +40955,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0eb137cd936bbfe0", @@ -25765,14 +40977,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25784,15 +40996,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b84fd6a0e2632ad9", @@ -25807,13 +41019,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25825,15 +41037,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "de9003e589631029", @@ -25848,13 +41060,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25866,15 +41078,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "326d4102190b74fc", @@ -25889,13 +41101,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25907,19 +41119,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "94b9287365ea4d0d", @@ -25934,27 +41146,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -25966,19 +41178,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "2f51a82838722bec", @@ -25993,27 +41205,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -26025,19 +41237,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "c9aff55e39e195e3", @@ -26052,27 +41264,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -26084,15 +41296,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "77d2adf5249eb826", @@ -26107,13 +41319,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -26125,15 +41337,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "503a2f4caacaf63e", @@ -26148,13 +41360,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -26166,15 +41378,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4176b9d43325a8d8", @@ -26189,13 +41401,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -26207,17 +41419,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2c5cae1389c11881", @@ -26232,15 +41444,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -26252,17 +41464,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "830eb4faff21eb0c", @@ -26277,15 +41489,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -26297,17 +41509,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9c24df68dc7d25a4", @@ -26322,15 +41534,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -26357,8 +41569,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -26385,8 +41597,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -26409,12 +41621,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", + "CONVERTER_interval_to_bedstrict_0", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "CONVERTER_interval_to_bedstrict_0", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2024-09-16", "versions": 1 @@ -26437,12 +41649,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", + "CONVERTER_interval_to_bedstrict_0", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "CONVERTER_interval_to_bedstrict_0", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2024-09-16", "versions": 2 @@ -26454,10 +41666,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "7d7550ce7004d71e", @@ -26472,13 +41684,13 @@ "imageanaylsis" ], "tools": [ - "ip_binary_to_labelimage", - "ip_overlay_images", "__EXTRACT_DATASET__", - "ip_filter_standard", + "ip_binary_to_labelimage", "ip_threshold", - "idr_download_by_ids", - "ip_histogram_equalization" + "ip_filter_standard", + "ip_histogram_equalization", + "ip_overlay_images", + "idr_download_by_ids" ], "update_time": "2024-09-13", "versions": 19 @@ -26504,9 +41716,9 @@ "tags": [], "tools": [ "gprofiler_gost", + "Cut1", "tp_split_on_column", - "goenrichment", - "Cut1" + "goenrichment" ], "update_time": "2024-09-10", "versions": 40 @@ -26520,14 +41732,14 @@ ], "doi": "", "edam_operation": [ - "Aggregation", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", + "Aggregation", + "Sequence composition calculation", "Taxonomic classification" ], "edam_topic": [], @@ -26543,14 +41755,14 @@ "microbiome" ], "tools": [ + "Filter1", "kraken2", - "porechop", - "nanoplot", - "taxonomy_krona_chart", + "krakentools_kreport2krona", "fastp", - "fastqc", - "Filter1", - "krakentools_kreport2krona" + "taxonomy_krona_chart", + "nanoplot", + "porechop", + "fastqc" ], "update_time": "2024-09-08", "versions": 0 @@ -26574,18 +41786,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", "collection_element_identifiers", "fgsea", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", - "oncoenrichr_wrapper", - "query_tabular", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "oncoenrichr_wrapper", + "decoupler_pseudobulk", + "query_tabular" ], "update_time": "2024-09-05", "versions": 1 @@ -26595,9 +41807,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -26613,13 +41825,13 @@ "epigenetics" ], "tools": [ - "bwa_mem", + "hicexplorer_hiccorrectmatrix", "hicexplorer_hicplotmatrix", - "hicexplorer_hicfindtads", + "hicexplorer_hicmergematrixbins", "hicexplorer_hicplottads", - "hicexplorer_hiccorrectmatrix", + "hicexplorer_hicfindtads", "hicexplorer_hicbuildmatrix", - "hicexplorer_hicmergematrixbins", + "bwa_mem", "hicexplorer_hicpca" ], "update_time": "2024-09-03", @@ -26679,27 +41891,27 @@ "name:public-data" ], "tools": [ - "anndata_ops", - "scanpy_read_10x", - "tp_grep_tool", - "scanpy_run_umap", + "scanpy_plot", + "scanpy_find_markers", "scanpy_filter_genes", - "scanpy_find_variable_genes", - "datamash_transpose", "join1", + "tp_grep_tool", + "scanpy_normalise_data", "scanpy_compute_graph", - "scanpy_plot_embed", - "scanpy_run_tsne", - "scanpy_find_markers", - "scanpy_find_cluster", - "scanpy_scale_data", - "scanpy_run_pca", + "regexColumn1", "retrieve_scxa", + "scanpy_find_variable_genes", + "scanpy_filter_cells", + "scanpy_run_umap", "anndata_inspect", - "scanpy_plot", - "regexColumn1", - "scanpy_normalise_data", - "scanpy_filter_cells" + "scanpy_run_tsne", + "scanpy_run_pca", + "scanpy_find_cluster", + "datamash_transpose", + "scanpy_read_10x", + "anndata_ops", + "scanpy_plot_embed", + "scanpy_scale_data" ], "update_time": "2024-09-01", "versions": 25 @@ -26726,11 +41938,11 @@ "earth-system" ], "tools": [ - "xarray_metadata_info", "xarray_coords_info", - "argo_getdata", + "timeseries_extraction", "interactive_tool_odv", - "timeseries_extraction" + "xarray_metadata_info", + "argo_getdata" ], "update_time": "2024-08-30", "versions": 15 @@ -26745,14 +41957,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "38f12705279b5dfa", @@ -26765,18 +41977,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", - "windowmasker_mkcounts", - "seqtk_telo", - "pick_value", - "minimap2", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "pick_value", + "fasta_compute_length" ], "update_time": "2024-08-28", "versions": 5 @@ -26791,14 +42003,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "efb58bba65393347", @@ -26811,18 +42023,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", - "windowmasker_mkcounts", - "seqtk_telo", - "pick_value", - "minimap2", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "pick_value", + "fasta_compute_length" ], "update_time": "2024-08-28", "versions": 32 @@ -26847,12 +42059,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "edu.tamu.cpt.genbank.shinefind", "promoter2", - "create_or_update", "iframe", - "jbrowse", + "create_or_update", + "edu.tamu.cpt.genbank.shinefind", "blast_reciprocal_best_hits", + "jbrowse", "get_orfs_or_cdss" ], "update_time": "2024-08-28", @@ -26876,11 +42088,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", - "anndata_manipulate", "scanpy_plot", + "anndata_manipulate", "scanpy_inspect", - "tp_cat" + "tp_cat", + "anndata_inspect" ], "update_time": "2024-08-23", "versions": 0 @@ -26901,8 +42113,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2024-08-21", "versions": 1 @@ -26929,8 +42141,8 @@ ], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2024-08-20", "versions": 2 @@ -26942,19 +42154,19 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Global alignment", + "Sequence contamination filtering", + "Phylogenetic tree generation", + "Sequence alignment", "Sequencing quality control", "Local alignment", + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment", "Variant calling", - "Phylogenetic tree generation", - "Sequence alignment", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", - "Taxonomic classification", + "Validation", "Phylogenetic tree visualisation", - "Sequence analysis", - "Validation" + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "2c79eee5ca5a3b09", @@ -26970,25 +42182,25 @@ "tuberculosis" ], "tools": [ - "tb_variant_filter", - "snippy", - "fastp", - "tp_sed_tool", - "mosdepth", + "EMBOSS: seqret84", + "tp_cat", "tbvcfreport", - "__FILTER_FAILED_DATASETS__", - "param_value_from_file", + "mosdepth", "qualimap_bamqc", - "__FLATTEN__", "Paste1", + "collection_element_identifiers", + "param_value_from_file", + "multiqc", + "__FLATTEN__", "tb_profiler_profile", "kraken2", - "tp_awk_tool", - "collection_element_identifiers", + "tb_variant_filter", + "snippy", "bcftools_consensus", - "EMBOSS: seqret84", - "multiqc", - "tp_cat" + "fastp", + "__FILTER_FAILED_DATASETS__", + "tp_sed_tool", + "tp_awk_tool" ], "update_time": "2024-08-19", "versions": 47 @@ -26998,10 +42210,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic analysis", "Sequence analysis", - "Multiple sequence alignment", - "Formatting" + "Phylogenetic analysis", + "Formatting", + "Multiple sequence alignment" ], "edam_topic": [], "id": "e97b938ca4723827", @@ -27015,9 +42227,9 @@ "tags": [], "tools": [ "picard_NormalizeFasta", - "snp_dists", + "rbc_mafft", "iqtree", - "rbc_mafft" + "snp_dists" ], "update_time": "2024-08-17", "versions": 1 @@ -27051,14 +42263,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree generation", + "Phylogenetic tree visualisation", "Phylogenetic inference", - "Phylogenetic tree reconstruction", "Taxonomic classification", "Phylogenetic tree analysis", - "Phylogenetic tree visualisation", - "Multiple sequence alignment", - "Phylogenetic tree generation", - "Phylogenetic tree editing" + "Phylogenetic tree reconstruction", + "Phylogenetic tree editing", + "Multiple sequence alignment" ], "edam_topic": [], "id": "ec50dd6d56f50db1", @@ -27071,10 +42283,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "graphlan", - "newick_display", "rbc_mafft", - "gd_raxml" + "graphlan", + "gd_raxml", + "newick_display" ], "update_time": "2024-08-15", "versions": 0 @@ -27084,16 +42296,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", + "Visualisation", "Statistical calculation", "Genome assembly", - "Coding region prediction" + "Sequence assembly visualisation", + "Sequencing quality control", + "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "a847773b563b2328", @@ -27106,12 +42318,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "prokka", "trimmomatic", + "spades", "bandage_image", "quast", - "prokka", - "fastqc", - "spades" + "fastqc" ], "update_time": "2024-08-13", "versions": 0 @@ -27139,17 +42351,17 @@ "metabolomics" ], "tools": [ - "qcxms_neutral_run", - "ctb_im_conformers", - "__FILTER_FAILED_DATASETS__", - "tp_cut_tool", "param_value_from_file", - "qcxms_getres", + "ctb_im_conformers", "xtb_molecular_optimization", + "__FILTER_FAILED_DATASETS__", "qcxms_production_run", - "openbabel_compound_convert", + "tp_cat", "split_file_to_collection", - "tp_cat" + "qcxms_getres", + "openbabel_compound_convert", + "tp_cut_tool", + "qcxms_neutral_run" ], "update_time": "2024-08-12", "versions": 2 @@ -27161,9 +42373,9 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", "Genome annotation", - "Sequence motif recognition" + "Sequence motif recognition", + "Protein feature detection" ], "edam_topic": [], "id": "b9c938d1af08124b", @@ -27181,9 +42393,9 @@ ], "tools": [ "interproscan", - "regex1", + "prodigal", "sanntis_marine", - "prodigal" + "regex1" ], "update_time": "2024-08-09", "versions": 5 @@ -27195,10 +42407,10 @@ ], "doi": "", "edam_operation": [ + "Differential gene expression analysis", "Dimensionality reduction", "Essential dynamics", - "Gene expression profiling", - "Differential gene expression analysis" + "Gene expression profiling" ], "edam_topic": [], "id": "e4e969e9943cdaa5", @@ -27215,18 +42427,18 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", "snapatac2_plotting", - "anndata_ops", "scanpy_plot", - "anndata_manipulate", - "scanpy_inspect", - "scanpy_filter", + "anndata_ops", "Cut1", + "scanpy_inspect", "scanpy_normalize", + "anndata_manipulate", "snapatac2_preprocessing", + "snapatac2_clustering", "replace_column_with_key_value_file", - "snapatac2_clustering" + "scanpy_filter", + "anndata_inspect" ], "update_time": "2024-08-08", "versions": 10 @@ -27269,21 +42481,21 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Sequencing quality control", - "Genome assembly", - "Variant calling", + "Genome annotation", + "Sequence contamination filtering", + "Visualisation", "Phylogenetic tree generation", + "Genome assembly", "Multilocus sequence typing", + "Sequencing quality control", + "Aggregation", + "Genome indexing", + "Validation", + "Variant calling", "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Genome annotation", - "Sequence contamination filtering", "Genome alignment", "Phylogenetic tree visualisation", - "Genome indexing", - "Validation", + "Antimicrobial resistance prediction", "Taxonomic classification" ], "edam_topic": [], @@ -27299,24 +42511,24 @@ "salmonella" ], "tools": [ - "abricate", - "abricate_summary", + "Filter1", "kraken2", "collapse_dataset", - "sistr_cmd", - "mlst", - "seqsero2", - "Cut1", - "snippy", - "quast", + "krakentools_kreport2krona", + "abricate", "bakta", - "taxonomy_krona_chart", + "seqsero2", "fastp", - "amrfinderplus", - "shovill", "multiqc", - "Filter1", - "krakentools_kreport2krona" + "abricate_summary", + "taxonomy_krona_chart", + "sistr_cmd", + "quast", + "amrfinderplus", + "snippy", + "Cut1", + "mlst", + "shovill" ], "update_time": "2024-08-02", "versions": 14 @@ -27329,20 +42541,20 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Sequencing quality control", - "Genome assembly", - "Variant calling", + "Genome annotation", + "Sequence contamination filtering", + "Visualisation", "Phylogenetic tree generation", + "Genome assembly", "Multilocus sequence typing", + "Sequencing quality control", + "Aggregation", + "Variant calling", "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Genome annotation", - "Sequence contamination filtering", - "Taxonomic classification", + "Validation", "Phylogenetic tree visualisation", - "Validation" + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "309fc4fc2e0da89c", @@ -27357,20 +42569,20 @@ "brucella" ], "tools": [ - "abricate", - "abricate_summary", + "Filter1", "kraken2", - "mlst", - "snippy", - "quast", + "krakentools_kreport2krona", + "abricate", "bakta", - "taxonomy_krona_chart", "fastp", - "amrfinderplus", - "shovill", "multiqc", - "Filter1", - "krakentools_kreport2krona" + "taxonomy_krona_chart", + "abricate_summary", + "quast", + "amrfinderplus", + "snippy", + "mlst", + "shovill" ], "update_time": "2024-08-02", "versions": 5 @@ -27382,17 +42594,17 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "De-novo assembly", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", - "Data retrieval", + "Sequence alignment", "Genome alignment", - "Genome indexing", + "Sequencing quality control", + "De-novo assembly", "Generation", - "Validation" + "Genome indexing", + "Data retrieval", + "Validation", + "Read mapping", + "Filtering" ], "edam_topic": [], "id": "629e57958afed44c", @@ -27408,22 +42620,22 @@ "virology" ], "tools": [ - "bwa_mem", + "param_value_from_file", "__EXTRACT_DATASET__", - "__FILTER_FAILED_DATASETS__", + "Show beginning1", "collapse_dataset", "tp_find_and_replace", - "read_it_and_keep", - "param_value_from_file", - "samtools_view", - "fasta_regex_finder", + "qualimap_bamqc", + "ivar_consensus", "fastp", - "multiqc", - "Show beginning1", "vapor", - "ivar_consensus", - "qualimap_bamqc", - "__FLATTEN__" + "__FILTER_FAILED_DATASETS__", + "multiqc", + "bwa_mem", + "__FLATTEN__", + "fasta_regex_finder", + "samtools_view", + "read_it_and_keep" ], "update_time": "2024-08-02", "versions": 9 @@ -27436,17 +42648,17 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Local alignment", - "Sequence alignment", + "Generation", "Genome indexing", - "Sequence contamination filtering", - "Global alignment", + "Sequence alignment analysis", "Sequence analysis", - "Generation", - "Validation" + "Global alignment", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "a31100610fba17a1", @@ -27462,31 +42674,31 @@ "virology" ], "tools": [ - "samtools_view", - "fastp", "samtools_merge", - "ivar_consensus", - "split_file_to_collection", - "tp_sed_tool", - "EMBOSS: maskseq51", - "datamash_ops", - "samtools_stats", - "__ZIP_COLLECTION__", - "__FILTER_FAILED_DATASETS__", - "param_value_from_file", - "compose_text_param", - "__SORTLIST__", + "Cut1", + "tp_cat", + "Grep1", "__APPLY_RULES__", "qualimap_bamqc", - "__FLATTEN__", - "fasta_compute_length", - "ivar_trim", - "bwa_mem", "collection_element_identifiers", - "Cut1", + "param_value_from_file", + "EMBOSS: maskseq51", "multiqc", - "Grep1", - "tp_cat" + "__SORTLIST__", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "fasta_compute_length", + "compose_text_param", + "ivar_consensus", + "__ZIP_COLLECTION__", + "samtools_stats", + "fastp", + "__FILTER_FAILED_DATASETS__", + "split_file_to_collection", + "tp_sed_tool", + "datamash_ops" ], "update_time": "2024-08-02", "versions": 0 @@ -27499,15 +42711,15 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", "Visualisation", - "Antimicrobial resistance prediction", "Statistical calculation", "Genome assembly", - "Validation" + "Sequencing quality control", + "Sequence composition calculation", + "Variant calling", + "Validation", + "Read mapping", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "4f245ac304ab76d9", @@ -27524,24 +42736,24 @@ "name:wgs" ], "tools": [ - "bcftools_norm", - "__FLATTEN__", - "abricate", - "trimmomatic", "regexColumn1", - "tp_awk_tool", + "bowtie2", "ggplot2_heatmap", "freebayes", - "Remove beginning1", + "trimmomatic", + "bcftools_norm", + "abricate", "multiqc", + "bcftools_view", + "Remove beginning1", + "vcf2tsv", "Grouping1", - "shovill", "collection_column_join", + "__FLATTEN__", "fastqc", - "bowtie2", - "vcf2tsv", - "bcftools_view", - "snpSift_filter" + "snpSift_filter", + "tp_awk_tool", + "shovill" ], "update_time": "2024-07-28", "versions": 16 @@ -27554,21 +42766,21 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Base position variability plotting", - "Sequence alignment analysis", - "De-novo assembly", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Phylogenetic analysis", - "Sequence alignment", - "Genome indexing", - "Sequence contamination filtering", "Sequence file editing", - "Data retrieval", "Multiple sequence alignment", + "De-novo assembly", + "Generation", + "Sequence alignment analysis", + "Genome indexing", "Sequence analysis", - "Generation" + "Data retrieval", + "Base position variability plotting", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "bc5ced57e711acf9", @@ -27584,32 +42796,32 @@ "virology" ], "tools": [ - "seqtk_subseq", - "samtools_view", - "fastp", - "__UNZIP_COLLECTION__", - "bamtools_split_ref", - "ivar_consensus", - "iqtree", - "__DUPLICATE_FILE_TO_COLLECTION__", - "snipit", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "pick_value", - "Show beginning1", "collapse_dataset", - "param_value_from_file", - "rbc_mafft", - "__APPLY_RULES__", + "tp_find_and_replace", "vapor", - "__RELABEL_FROM_FILE__", - "map_param_value", + "Grep1", + "__APPLY_RULES__", "qualimap_bamqc", "Paste1", - "bwa_mem", - "wc_gnu", "collection_element_identifiers", - "Grep1" + "param_value_from_file", + "rbc_mafft", + "wc_gnu", + "Show beginning1", + "bamtools_split_ref", + "bwa_mem", + "samtools_view", + "__UNZIP_COLLECTION__", + "pick_value", + "iqtree", + "__DUPLICATE_FILE_TO_COLLECTION__", + "ivar_consensus", + "seqtk_subseq", + "__RELABEL_FROM_FILE__", + "fastp", + "map_param_value", + "snipit" ], "update_time": "2024-07-28", "versions": 21 @@ -27641,20 +42853,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly", + "Genome annotation", + "Statistical calculation", + "Read binning", + "Sequence clustering", + "Visualisation", "Genome comparison", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Sequence assembly", "Genome assembly", + "Sequencing quality control", "Local alignment", - "Read binning", + "Sequence composition calculation", "Sequence assembly validation", - "Genome annotation", - "Visualisation", - "Statistical calculation", - "Sequence clustering", - "Validation" + "Validation", + "Read mapping" ], "edam_topic": [], "id": "97312d273b6e8bd9", @@ -27669,26 +42881,26 @@ "name:microgalaxy" ], "tools": [ - "concoct_extract_fasta_bins", - "maxbin2", - "Fasta_to_Contig2Bin", "fastq_paired_end_interlacer", + "checkm_lineage_wf", + "concoct_cut_up_fasta", + "bowtie2", + "drep_dereplicate", "samtools_sort", - "__UNZIP_COLLECTION__", - "megahit", - "coverm_genome", "concoct_merge_cut_up_clustering", - "drep_dereplicate", - "concoct", - "metabat2", "semibin", "quast", + "__UNZIP_COLLECTION__", + "concoct_extract_fasta_bins", + "metabat2", + "megahit", + "concoct", "metabat2_jgi_summarize_bam_contig_depths", - "checkm_lineage_wf", + "Fasta_to_Contig2Bin", + "coverm_genome", "das_tool", - "concoct_coverage_table", - "concoct_cut_up_fasta", - "bowtie2" + "maxbin2", + "concoct_coverage_table" ], "update_time": "2024-07-11", "versions": 14 @@ -27711,9 +42923,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scanpy_cluster_reduce_dimension", + "scanpy_plot", "scanpy_inspect", - "scanpy_plot" + "scanpy_cluster_reduce_dimension" ], "update_time": "2024-07-08", "versions": 0 @@ -27752,13 +42964,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Validation", "Sequencing quality control", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "c7f34c67c9054234", @@ -27771,20 +42983,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "__FILTER_FAILED_DATASETS__", - "collection_element_identifiers", - "__FILTER_EMPTY_DATASETS__", - "tp_sorted_uniq", - "compress_file", + "Paste1", "fastq_filter", - "multiqc", - "__RELABEL_FROM_FILE__", + "collection_element_identifiers", "fastqc", "ncbi_blastn_wrapper", "regex_replace", + "multiqc", + "__FILTER_FAILED_DATASETS__", + "compress_file", + "__FILTER_EMPTY_DATASETS__", + "ab1_fastq_converter", + "tp_sorted_uniq", "cutadapt", - "Paste1", - "ab1_fastq_converter" + "__RELABEL_FROM_FILE__" ], "update_time": "2024-07-03", "versions": 6 @@ -27797,9 +43009,9 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", "Genome visualisation", - "Sequence motif recognition" + "Sequence motif recognition", + "Protein feature detection" ], "edam_topic": [], "id": "df7d9943423549df", @@ -27816,23 +43028,23 @@ "apollo" ], "tools": [ - "interproscan", - "create_or_update", - "edu.tamu.cpt.gff3.require_phage_start", + "edu.tamu.cpt.gff3.export_seq", + "edu.tamu.cpt.gff3.cdsParents", "fetch_jbrowse", - "gff3.rebase", "ncbi_blastp_wrapper", - "edu.tamu.cpt.fasta.seq_trans", - "edu.tamu.cpt.gff3.cdsParents", + "blastxml_to_gapped_gff3", + "gff3.rebase", + "edu.tamu.cpt.fasta.lipory", + "cshl_fasta_formatter", "edu.tamu.cpt.fasta.remove_desc", + "edu.tamu.cpt.fasta.seq_trans", + "edu.tamu.cpt.gff3.require_phage_start", + "create_or_update", "iframe", - "cshl_fasta_formatter", + "edu.tamu.cpt.gff3.remove_annots", + "interproscan", "jbrowse", - "blastxml_to_gapped_gff3", - "edu.tamu.cpt.fasta.lipory", - "edu.tamu.cpt.gff3.export_seq", - "get_orfs_or_cdss", - "edu.tamu.cpt.gff3.remove_annots" + "get_orfs_or_cdss" ], "update_time": "2024-07-02", "versions": 1 @@ -27857,11 +43069,11 @@ "eebg24" ], "tools": [ - "tp_easyjoin_tool", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "tp_easyjoin_tool", + "datamash_ops" ], "update_time": "2024-07-02", "versions": 2 @@ -27882,12 +43094,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "eal_table_template", - "fasta2tab", - "makeeml", "__MERGE_COLLECTION__", "__BUILD_LIST__", - "tp_cat" + "eal_table_template", + "fasta2tab", + "tp_cat", + "makeeml" ], "update_time": "2024-07-01", "versions": 0 @@ -27911,8 +43123,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bowtie2", - "htseq_count" + "htseq_count", + "bowtie2" ], "update_time": "2024-06-30", "versions": 3 @@ -27922,9 +43134,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequencing quality control", "Read mapping", - "Nucleic acid sequence analysis", - "Sequencing quality control" + "Nucleic acid sequence analysis" ], "edam_topic": [], "id": "0821ec1cb4d6f30b", @@ -27937,8 +43149,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bowtie2", "htseq_count", + "bowtie2", "umi_tools_count" ], "update_time": "2024-06-30", @@ -27949,17 +43161,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", - "RNA-Seq analysis", + "Sequence alignment", + "Differential gene expression analysis", "Gene functional annotation", + "Sequencing quality control", + "Sequence composition calculation", "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "20ada53472782c9b", @@ -27972,33 +43184,33 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "volcanoplot", - "rseqc_read_distribution", + "rseqc_junction_annotation", + "trimmomatic", + "join1", "fastqc", - "samtools_idxstats", - "tp_replace_in_line", - "sort1", - "Show beginning1", - "deseq2", + "rna_star", + "__TAG_FROM_FILE__", + "collection_element_identifiers", + "Filter1", "Add_a_column1", - "join1", + "sort1", + "samtools_idxstats", "featurecounts", - "gtftobed12", + "Show beginning1", + "multiqc", "Convert characters1", - "__RELABEL_FROM_FILE__", - "goseq", - "tp_replace_in_column", + "deseq2", "cat1", - "ggplot2_heatmap2", - "rseqc_junction_annotation", - "trimmomatic", - "rna_star", - "collection_element_identifiers", - "Cut1", - "__TAG_FROM_FILE__", + "tp_replace_in_line", + "tp_replace_in_column", + "__RELABEL_FROM_FILE__", + "rseqc_read_distribution", + "gtftobed12", "Remove beginning1", - "multiqc", - "Filter1" + "volcanoplot", + "Cut1", + "ggplot2_heatmap2", + "goseq" ], "update_time": "2024-06-29", "versions": 4 @@ -28014,12 +43226,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "376119528377a3ae", @@ -28037,28 +43249,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-06-24", "versions": 58 @@ -28091,24 +43303,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-06-24", "versions": 72 @@ -28122,19 +43334,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "a705370bc2c13d5c", @@ -28153,23 +43365,23 @@ "name:iwc" ], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-06-24", "versions": 190 @@ -28200,9 +43412,9 @@ "name:gtn" ], "tools": [ + "interactive_tool_phinch", "kraken_biom", - "kraken2", - "interactive_tool_phinch" + "kraken2" ], "update_time": "2024-06-19", "versions": 8 @@ -28212,11 +43424,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", "Visualisation", "Prediction and recognition", - "Formatting" + "Filtering", + "Formatting", + "Label-free quantification" ], "edam_topic": [], "id": "fc42cc9467c6ee8d", @@ -28233,17 +43445,17 @@ ], "tools": [ "msconvert", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", "regex1", + "query_tabular", "unipept", "tp_replace_in_line", + "search_gui", "Remove beginning1", - "query_tabular", + "tp_replace_in_column", "flashlfq", - "Filter1", - "tp_replace_in_column" + "Cut1", + "peptide_shaker" ], "update_time": "2024-06-19", "versions": 0 @@ -28274,9 +43486,9 @@ "ospd" ], "tools": [ + "hirondelle_crim", "cat1", - "otb_band_math", - "hirondelle_crim" + "otb_band_math" ], "update_time": "2024-06-19", "versions": 15 @@ -28289,10 +43501,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -28306,9 +43518,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "qiime2__feature_classifier__classify_sklearn", "qiime2__metadata__tabulate", - "qiime2__taxa__barplot", - "qiime2__feature_classifier__classify_sklearn" + "qiime2__taxa__barplot" ], "update_time": "2024-06-18", "versions": 1 @@ -28321,10 +43533,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -28339,10 +43551,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-06-18", "versions": 2 @@ -28355,10 +43567,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -28377,8 +43589,8 @@ ], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-06-18", "versions": 1 @@ -28391,10 +43603,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -28429,10 +43641,10 @@ "doi": "", "edam_operation": [ "Visualisation", - "Taxonomic classification", "Sequencing quality control", "Phylogenetic analysis", - "Demultiplexing" + "Demultiplexing", + "Taxonomic classification" ], "edam_topic": [], "id": "6ad6d87618c4e405", @@ -28457,8 +43669,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis" + "Sequence alignment analysis", + "Data handling" ], "edam_topic": [], "id": "e522be58f0bac656", @@ -28471,9 +43683,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bbgtobigwig", - "winnowmap", "meryl", + "winnowmap", + "bbgtobigwig", "bamFilter", "fasta_compute_length" ], @@ -28490,14 +43702,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "aada0111f835ce49", @@ -28510,19 +43722,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", + "repeatmasker_wrapper", + "gfastats", + "jbrowse2", + "bedtools_makewindowsbed", "windowmasker_mkcounts", "gff2bed1", - "seqtk_telo", - "pick_value", "minimap2", - "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", - "jbrowse2", - "gfastats" + "pick_value", + "fasta_compute_length" ], "update_time": "2024-06-14", "versions": 22 @@ -28545,13 +43757,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sort1", + "tp_head_tool", + "bedtools_intersectbed", "CONVERTER_bed_to_fli_0", "comp1", "datamash_ops", - "sort1", - "CONVERTER_interval_to_bgzip_0", - "tp_head_tool", - "bedtools_intersectbed" + "CONVERTER_interval_to_bgzip_0" ], "update_time": "2024-06-12", "versions": 0 @@ -28577,20 +43789,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-06-10", "versions": 0 @@ -28615,9 +43827,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", + "ucsc_wigtobigwig", "bedtools_coveragebed", - "ucsc_wigtobigwig" + "Cut1" ], "update_time": "2024-06-09", "versions": 40 @@ -28629,11 +43841,11 @@ ], "doi": "", "edam_operation": [ - "Genome visualisation", - "Data handling", "Sequence alignment analysis", "Pathway visualisation", - "Structure visualisation" + "Genome visualisation", + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "2cd5670f075704ab", @@ -28646,11 +43858,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "winnowmap", "meryl", + "winnowmap", + "jbrowse2", "CONVERTER_bam_to_bigwig_0", - "bamFilter", - "jbrowse2" + "bamFilter" ], "update_time": "2024-06-08", "versions": 5 @@ -28678,13 +43890,13 @@ "metabolomics" ], "tools": [ - "qcxms_neutral_run", - "ctb_im_conformers", - "__FILTER_FAILED_DATASETS__", - "qcxms_getres", "xtb_molecular_optimization", + "__FILTER_FAILED_DATASETS__", "qcxms_production_run", - "openbabel_compound_convert" + "qcxms_getres", + "openbabel_compound_convert", + "ctb_im_conformers", + "qcxms_neutral_run" ], "update_time": "2024-06-06", "versions": 64 @@ -28698,15 +43910,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "585c21b7b1d864fc", @@ -28724,18 +43936,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-06-05", "versions": 142 @@ -28749,9 +43961,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "10101558b211a782", @@ -28769,8 +43981,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-06-05", @@ -28792,17 +44004,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seurat_find_variable_genes", "seurat_scale_data", "seurat_find_neighbours", - "seurat_normalise_data", - "seurat_run_umap", - "seurat_plot", + "retrieve_scxa", "seurat_run_pca", + "seurat_normalise_data", "seurat_find_clusters", "seurat_filter_cells", - "seurat_read10x", - "retrieve_scxa" + "seurat_plot", + "seurat_run_umap", + "seurat_find_variable_genes", + "seurat_read10x" ], "update_time": "2024-06-03", "versions": 0 @@ -28814,14 +44026,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "9eda857e4141d56e", @@ -28837,18 +44049,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-29", "versions": 0 @@ -28860,14 +44072,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "cd926dd6b70e72d6", @@ -28883,18 +44095,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-29", "versions": 0 @@ -28906,16 +44118,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "529f30e894beacc2", @@ -28933,27 +44145,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2024-05-29", "versions": 0 @@ -28965,14 +44177,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "112422839b68db02", @@ -28989,18 +44201,18 @@ "cloud-costs" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-28", "versions": 0 @@ -29010,17 +44222,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "67e20e3082d24fbd", @@ -29033,23 +44245,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "ggplot2_heatmap2", + "Filter1", "gffread", - "Cut1", - "tp_cut_tool", - "trim_galore", + "gprofiler_gost", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", - "join1", + "fasterq_dump", + "trim_galore", + "Grep1", + "column_order_header_sort", "collection_column_join", + "join1", "fastqc", - "column_order_header_sort", - "Filter1", - "Grep1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2024-05-27", "versions": 5 @@ -29059,18 +44271,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Editing", - "Sequence annotation", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", + "Editing", + "Scaffolding", "Differential protein expression profiling", - "RNA-Seq analysis", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9fb31a16b258cc1a", @@ -29089,13 +44301,13 @@ ], "tools": [ "jcvi_gff_stats", - "omark", "gffread", + "compleasm", "helixer", "red", - "compleasm", "busco", - "jbrowse" + "jbrowse", + "omark" ], "update_time": "2024-05-27", "versions": 20 @@ -29122,10 +44334,10 @@ "satellite" ], "tools": [ - "srs_diversity_maps", - "srs_global_indices", + "srs_spectral_indices", "srs_preprocess_s2", - "srs_spectral_indices" + "srs_global_indices", + "srs_diversity_maps" ], "update_time": "2024-05-27", "versions": 5 @@ -29135,17 +44347,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "2f37c35ade97aa8d", @@ -29158,23 +44370,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "ggplot2_heatmap2", + "Filter1", "gffread", - "Cut1", - "tp_cut_tool", - "trim_galore", + "gprofiler_gost", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", - "join1", + "fasterq_dump", + "trim_galore", + "Grep1", + "column_order_header_sort", "collection_column_join", + "join1", "fastqc", - "column_order_header_sort", - "Filter1", - "Grep1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2024-05-27", "versions": 1 @@ -29184,17 +44396,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "21dd4bd16579fc12", @@ -29210,23 +44422,23 @@ "2024" ], "tools": [ - "gprofiler_gost", + "Paste1", "limma_voom", - "ggplot2_heatmap2", + "Filter1", "gffread", - "Cut1", - "join1", - "trim_galore", + "gprofiler_gost", + "ggplot2_heatmap2", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", - "tp_cut_tool", + "fasterq_dump", + "trim_galore", "collection_column_join", - "__RELABEL_FROM_FILE__", + "join1", "fastqc", - "Filter1", - "Paste1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-26", "versions": 3 @@ -29238,10 +44450,10 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "510bcef37f385495", @@ -29258,14 +44470,14 @@ ], "tools": [ "CONVERTER_bed_gff_or_vcf_to_bigwig_0", - "fastqc", - "tp_sort_header_tool", - "stacks2_procrad", - "stacks2_populations", + "Filter1", + "tp_head_tool", "multiqc", + "stacks2_populations", + "tp_sort_header_tool", + "fastqc", "stacks2_denovomap", - "tp_head_tool", - "Filter1" + "stacks2_procrad" ], "update_time": "2024-05-23", "versions": 4 @@ -29275,12 +44487,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "d086340422009ba9", @@ -29295,9 +44507,9 @@ "tools": [ "htseq_count", "multiqc", - "hisat2", + "__FLATTEN__", "fastqc", - "__FLATTEN__" + "hisat2" ], "update_time": "2024-05-19", "versions": 2 @@ -29307,13 +44519,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "2fd462d85412444c", @@ -29326,10 +44538,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "cutadapt", "multiqc", - "fastqc", "__FLATTEN__", - "cutadapt" + "fastqc" ], "update_time": "2024-05-18", "versions": 1 @@ -29339,10 +44551,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "0ec684b341ad172d", @@ -29361,8 +44573,8 @@ "qualitycheck" ], "tools": [ - "fastqc", - "multiqc" + "multiqc", + "fastqc" ], "update_time": "2024-05-17", "versions": 8 @@ -29372,16 +44584,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Genome assembly", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", + "Genome assembly", "Scaffolding", - "Transcriptome assembly", + "Sequence annotation", "Differential protein expression profiling", + "Transcriptome assembly", "Sequence analysis", + "Sequence assembly validation", + "Genome visualisation", "Repeat sequence detection" ], "edam_topic": [], @@ -29400,14 +44612,14 @@ ], "tools": [ "jcvi_gff_stats", - "omark", "gffread", + "compleasm", "helixer", "repeatmodeler", - "compleasm", "repeatmasker_wrapper", "busco", - "jbrowse" + "jbrowse", + "omark" ], "update_time": "2024-05-15", "versions": 6 @@ -29428,19 +44640,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Visualisation", - "Read summarisation", "Statistical calculation", + "Visualisation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Sequence trimming", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling" ], "edam_topic": [], "id": "985044b4b2c51425", @@ -29455,25 +44667,25 @@ "transcriptomics" ], "tools": [ - "rseqc_read_distribution", - "samtools_view", - "rseqc_infer_experiment", + "rseqc_geneBody_coverage", + "tp_tail_tool", "fastqc", - "samtools_idxstats", + "rna_star", + "rseqc_infer_experiment", "__MERGE_COLLECTION__", - "tp_sort_header_tool", "featurecounts", - "gtftobed12", + "samtools_idxstats", + "multiqc", + "tp_sort_header_tool", "__FLATTEN__", - "tp_tail_tool", + "length_and_gc_content", + "cutadapt", + "samtools_view", "picard_MarkDuplicates", - "rna_star", + "rseqc_read_distribution", + "gtftobed12", "Cut1", - "pygenomeTracks", - "length_and_gc_content", - "rseqc_geneBody_coverage", - "multiqc", - "cutadapt" + "pygenomeTracks" ], "update_time": "2024-05-13", "versions": 0 @@ -29494,19 +44706,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Visualisation", - "Read summarisation", "Statistical calculation", + "Visualisation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "a28c207730e7e13d", @@ -29521,23 +44733,23 @@ "transcriptomics" ], "tools": [ - "picard_MarkDuplicates", - "tp_sort_header_tool", - "rna_star", - "rseqc_read_distribution", - "Cut1", + "rseqc_geneBody_coverage", "featurecounts", - "pygenomeTracks", - "rseqc_infer_experiment", - "gtftobed12", - "length_and_gc_content", + "samtools_idxstats", + "tp_tail_tool", + "Cut1", "multiqc", - "rseqc_geneBody_coverage", - "fastqc", + "gtftobed12", + "tp_sort_header_tool", "__FLATTEN__", - "samtools_idxstats", + "fastqc", + "rna_star", + "length_and_gc_content", "cutadapt", - "tp_tail_tool" + "rseqc_infer_experiment", + "pygenomeTracks", + "rseqc_read_distribution", + "picard_MarkDuplicates" ], "update_time": "2024-05-13", "versions": 0 @@ -29547,17 +44759,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "fe64d430d50faf0b", @@ -29570,23 +44782,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "ggplot2_heatmap2", + "Filter1", "gffread", - "Cut1", - "tp_cut_tool", - "trim_galore", + "gprofiler_gost", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", - "join1", + "fasterq_dump", + "trim_galore", + "Grep1", + "column_order_header_sort", "collection_column_join", + "join1", "fastqc", - "column_order_header_sort", - "Filter1", - "Grep1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2024-05-08", "versions": 0 @@ -29596,17 +44808,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6fc2b9bea5b75a49", @@ -29619,23 +44831,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "ggplot2_heatmap2", + "Filter1", "gffread", - "Cut1", - "join1", - "trim_galore", - "tp_cut_tool", - "fasterq_dump", - "salmon", + "gprofiler_gost", "tp_find_and_replace", + "tp_tail_tool", + "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", + "column_order_header_sort", "collection_column_join", + "join1", "fastqc", - "column_order_header_sort", - "Filter1", - "Grep1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2024-05-08", "versions": 0 @@ -29645,11 +44857,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence contamination filtering", + "Statistical calculation", "Sequence alignment", - "Sequencing quality control", "Variant calling", + "Sequencing quality control", "Formatting" ], "edam_topic": [], @@ -29663,17 +44875,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", + "freebayes", + "snpEff", "Add_a_column1", - "rna_star", + "fastp", + "picard_AddOrReplaceReadGroups", "vcf2tsv", - "snpEff", - "freebayes", - "vcfcombine", "tp_unfold_column_tool", - "fastp", - "Filter1", "snpSift_annotate", - "picard_AddOrReplaceReadGroups" + "rna_star", + "vcfcombine" ], "update_time": "2024-05-08", "versions": 13 @@ -29683,16 +44895,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Sequence contamination filtering", - "Statistical calculation", - "Nucleic acid sequence analysis" + "Data handling" ], "edam_topic": [], "id": "b6eb5fe7e37f680a", @@ -29706,15 +44918,15 @@ "tags": [], "tools": [ "sickle", - "trimmomatic", - "fastq_quality_trimmer", - "trim_galore", - "fastq_dump", "htseq_count", "samtools_stats", + "fastq_quality_trimmer", + "trimmomatic", "fastp", + "trim_galore", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2024-05-08", "versions": 24 @@ -29726,10 +44938,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", "Image analysis", + "Image annotation", "Visualisation", - "Image annotation" + "Data handling" ], "edam_topic": [], "id": "e87e726b57f1a875", @@ -29746,9 +44958,9 @@ "preprocessing" ], "tools": [ - "tp_split_on_column", + "ip_threshold", "param_value_from_file", - "ip_threshold" + "tp_split_on_column" ], "update_time": "2024-05-05", "versions": 4 @@ -29760,10 +44972,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "1ffacb28226460ac", @@ -29780,15 +44992,15 @@ "segmentation" ], "tools": [ + "ip_2d_feature_extraction", "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", - "ip_2d_filter_segmentation_by_features", "ip_filter_standard", - "ip_convertimage", - "ip_threshold", "ip_histogram_equalization", - "ip_2d_feature_extraction" + "ip_convertimage", + "ip_2d_filter_segmentation_by_features", + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-05-05", "versions": 9 @@ -29803,14 +45015,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "5f29105e842716db", @@ -29823,19 +45035,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", - "windowmasker_ustat", - "windowmasker_mkcounts", "mashmap", - "seqtk_telo", - "pick_value", - "minimap2", + "deeptools_bam_coverage", + "windowmasker_ustat", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "pick_value", + "fasta_compute_length" ], "update_time": "2024-05-02", "versions": 40 @@ -29872,14 +45084,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "3cf3dd9727b7ac92", @@ -29892,19 +45104,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", - "windowmasker_ustat", - "windowmasker_mkcounts", "mashmap", - "seqtk_telo", - "pick_value", - "minimap2", + "deeptools_bam_coverage", + "windowmasker_ustat", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "pick_value", + "fasta_compute_length" ], "update_time": "2024-04-27", "versions": 26 @@ -29914,35 +45126,35 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", + "Visualisation", + "Sequence motif recognition", + "Gene functional annotation", "Sequence assembly", - "Coding region prediction", + "Database search", + "Primer removal", "Sequencing quality control", + "Format validation", "Formatting", - "Visualisation", - "Data retrieval", - "Read pre-processing", - "Sequence trimming", - "Database search", - "Gene functional annotation", - "Sequence profile generation", - "Protein feature detection", "Aggregation", - "Format validation", - "Sequence composition calculation", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence analysis", "Sequence database search", - "Local alignment", + "Sequence trimming", "Sequence assembly validation", + "Sequence profile generation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", - "Primer removal", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment", - "Sequence analysis", - "Validation" + "Local alignment", + "Sequence composition calculation", + "Read pre-processing", + "Sequence generation", + "Data retrieval", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "8deb08d4f228e198", @@ -29955,26 +45167,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "maxbin2", - "trim_galore", + "kofamscan", + "tp_cat", + "checkm_lineage_wf", + "fastqc", "tp_grep_tool", + "sort1", + "krakentools_kreport2krona", + "quast", + "fraggenescan", + "kraken2", "taxonomy_krona_chart", - "fastqc", + "trim_galore", + "coverm_contig", + "cat_bins", "coverm_genome", "fasplit", - "fraggenescan", "hmmer_hmmscan", - "sort1", - "coverm_contig", "interproscan", - "quast", - "kofamscan", - "checkm_lineage_wf", - "cat_bins", - "kraken2", - "tp_awk_tool", - "krakentools_kreport2krona", - "tp_cat" + "maxbin2", + "tp_awk_tool" ], "update_time": "2024-04-25", "versions": 1 @@ -29984,17 +45196,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Sequence assembly", - "De-novo assembly", - "Variant calling", - "Box-Whisker plot plotting", - "Sequence assembly validation", "Visualisation", "Genome assembly", + "Scatter plot plotting", + "Sequence assembly", "Mapping assembly", + "Base-calling", "Cross-assembly", - "Base-calling" + "Box-Whisker plot plotting", + "De-novo assembly", + "Variant calling", + "Sequence assembly validation" ], "edam_topic": [], "id": "34a07bf6407510ef", @@ -30011,9 +45223,9 @@ ], "tools": [ "medaka_consensus_pipeline", - "nanoplot", "flye", - "quast" + "quast", + "nanoplot" ], "update_time": "2024-04-24", "versions": 15 @@ -30025,14 +45237,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "2e93613c688ea52e", @@ -30045,19 +45257,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", "Add_a_column1", - "windowmasker_ustat", - "windowmasker_mkcounts", "mashmap", - "seqtk_telo", - "pick_value", - "minimap2", + "deeptools_bam_coverage", + "windowmasker_ustat", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "pick_value", + "fasta_compute_length" ], "update_time": "2024-04-23", "versions": 34 @@ -30082,8 +45294,8 @@ ], "tools": [ "tp_cut_tool", - "join1", - "tp_find_and_replace" + "tp_find_and_replace", + "join1" ], "update_time": "2024-04-22", "versions": 20 @@ -30095,14 +45307,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", "Mapping", + "Pairwise sequence alignment", + "Pathway visualisation", + "Genome visualisation", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Data handling" ], "edam_topic": [], "id": "cc2bc81352d2e2cd", @@ -30115,18 +45327,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", + "seqtk_telo", + "mashmap", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", - "windowmasker_mkcounts", - "mashmap", - "seqtk_telo", - "minimap2", + "gfastats", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "fasta_compute_length" ], "update_time": "2024-04-19", "versions": 20 @@ -30140,10 +45352,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "af472984b3f3d65f", @@ -30158,20 +45370,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-04-18", "versions": 1 @@ -30185,10 +45397,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8c4331f1bac67aba", @@ -30203,19 +45415,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-18", "versions": 1 @@ -30229,10 +45441,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "895b8f5736bb92bb", @@ -30247,19 +45459,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-18", "versions": 1 @@ -30286,8 +45498,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-18", "versions": 1 @@ -30298,9 +45510,9 @@ "doi": "", "edam_operation": [ "Sequence assembly validation", - "Transcriptome assembly", "Scaffolding", - "Genome assembly" + "Genome assembly", + "Transcriptome assembly" ], "edam_topic": [], "id": "c9a8fba4c56f5c83", @@ -30314,8 +45526,8 @@ "tags": [], "tools": [ "interactive_tool_blobtoolkit", - "busco", - "blobtoolkit" + "blobtoolkit", + "busco" ], "update_time": "2024-04-17", "versions": 0 @@ -30325,8 +45537,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein feature detection", - "Sequence motif recognition" + "Sequence motif recognition", + "Protein feature detection" ], "edam_topic": [], "id": "9a95556ec171d405", @@ -30343,8 +45555,8 @@ ], "tools": [ "gbk_to_orf", - "interproscan", "ncbi_blastp_wrapper", + "interproscan", "edu.tamu.cpt.gff.gff2gb" ], "update_time": "2024-04-16", @@ -30372,10 +45584,10 @@ "smallorfs" ], "tools": [ - "edu.tamu.cpt.gff3.require_phage_start", + "edu.tamu.cpt.gff3.export_seq", "edu.tamu.cpt.gff3.cdsParents", + "edu.tamu.cpt.gff3.require_phage_start", "edu.tamu.cpt.fasta.remove_desc", - "edu.tamu.cpt.gff3.export_seq", "get_orfs_or_cdss" ], "update_time": "2024-04-15", @@ -30386,25 +45598,25 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence annotation", - "Sequencing quality control", - "Differential gene expression analysis", - "Formatting", - "Fold recognition", + "Genome annotation", "Homology-based gene prediction", - "Query and retrieval", - "Data retrieval", - "Sequence composition calculation", - "Sequence database search", + "Information extraction", "Sequence alignment", - "Genome annotation", + "Fold recognition", + "Sequencing quality control", + "Formatting", "Read summarisation", + "Sequence database search", + "Data handling", "Statistical calculation", - "RNA-Seq analysis", - "Information extraction", + "Differential gene expression analysis", + "Query and retrieval", + "Sequence composition calculation", + "Data retrieval", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "c5e6047b3b256b06", @@ -30417,26 +45629,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "picard_NormalizeFasta", "eggnog_mapper", "fastqc", - "Extract genomic DNA 1", - "gffread", + "rna_star", + "__TAG_FROM_FILE__", + "collection_element_identifiers", + "Add_a_column1", + "featurecounts", "regex1", - "tp_replace_in_line", + "multiqc", + "Extract genomic DNA 1", + "deg_annotate", "comp1", "deseq2", - "Add_a_column1", - "picard_NormalizeFasta", - "featurecounts", - "trimmer", + "gffread", + "tp_head_tool", + "tp_replace_in_line", "datasets_download_genome", - "rna_star", - "collection_element_identifiers", "Cut1", - "__TAG_FROM_FILE__", - "deg_annotate", - "multiqc", - "tp_head_tool" + "trimmer" ], "update_time": "2024-04-14", "versions": 0 @@ -30446,15 +45658,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Differential gene expression analysis", "Sequence alignment", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "250e6058f160825f", @@ -30467,14 +45679,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", "collection_element_identifiers", - "trimmer", "featurecounts", - "__TAG_FROM_FILE__", + "deseq2", "multiqc", "fastqc", - "deseq2" + "rna_star", + "__TAG_FROM_FILE__", + "trimmer" ], "update_time": "2024-04-14", "versions": 0 @@ -30484,18 +45696,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Editing", - "Sequence annotation", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", - "Scaffolding", "Genome assembly", + "Editing", + "Scaffolding", "Differential protein expression profiling", - "RNA-Seq analysis", + "Transcriptome assembly", "Sequence analysis", - "Transcriptome assembly" + "Sequence assembly validation", + "Genome visualisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3d604dad4f1f5b3d", @@ -30515,12 +45727,12 @@ "tools": [ "jcvi_gff_stats", "gffread", - "omark", + "compleasm", "helixer", "red", - "compleasm", "busco", - "jbrowse" + "jbrowse", + "omark" ], "update_time": "2024-04-11", "versions": 3 @@ -30530,16 +45742,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Genome assembly", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", "Genome annotation", + "Genome assembly", "Scaffolding", - "Transcriptome assembly", + "Sequence annotation", "Differential protein expression profiling", + "Transcriptome assembly", "Sequence analysis", + "Sequence assembly validation", + "Genome visualisation", "Repeat sequence detection" ], "edam_topic": [], @@ -30561,13 +45773,13 @@ "tools": [ "jcvi_gff_stats", "gffread", - "omark", + "compleasm", "helixer", "repeatmodeler", - "compleasm", "repeatmasker_wrapper", "busco", - "jbrowse" + "jbrowse", + "omark" ], "update_time": "2024-04-11", "versions": 9 @@ -30583,11 +45795,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "0f563f176bb245af", @@ -30635,9 +45847,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-04-11", "versions": 1 @@ -30650,8 +45862,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "967f890c0883f72a", @@ -30664,8 +45876,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-04-11", "versions": 1 @@ -30678,8 +45890,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "2da3c41ad5c11c3b", @@ -30707,10 +45919,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4cb25c0bb103f54f", @@ -30725,20 +45937,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-04-11", "versions": 1 @@ -30752,10 +45964,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "66f2a58637054c16", @@ -30770,19 +45982,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-11", "versions": 1 @@ -30796,10 +46008,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8ff9d3ad20e87819", @@ -30814,19 +46026,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-11", "versions": 1 @@ -30838,15 +46050,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "166eb3f14feffa1b", @@ -30861,13 +46073,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-04-11", "versions": 1 @@ -30879,19 +46091,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "93a7047396080fda", @@ -30906,27 +46118,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-04-11", "versions": 1 @@ -30938,15 +46150,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1c44bbaa5f4f8b54", @@ -30961,13 +46173,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-04-11", "versions": 1 @@ -30979,17 +46191,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f6b55599db1ab056", @@ -31004,15 +46216,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-04-11", "versions": 1 @@ -31040,8 +46252,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-11", "versions": 1 @@ -31051,11 +46263,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Sequencing quality control", "Sequence alignment", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control", + "Read summarisation" ], "edam_topic": [], "id": "3550384e7c062a60", @@ -31068,9 +46280,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "hisat2", "multiqc", - "featurecounts", - "hisat2" + "featurecounts" ], "update_time": "2024-04-08", "versions": 2 @@ -31080,11 +46292,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Gene expression analysis", "Sequence composition calculation", + "Gene expression analysis", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling" ], "edam_topic": [], "id": "0d6bed63a2e4c3d6", @@ -31098,10 +46310,10 @@ "tags": [], "tools": [ "trimmomatic", - "rna_star", - "fasterq_dump", "samtools_sort", - "salmon" + "salmon", + "fasterq_dump", + "rna_star" ], "update_time": "2024-04-08", "versions": 9 @@ -31124,13 +46336,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2024-04-07", "versions": 2 @@ -31157,17 +46369,17 @@ "apollo" ], "tools": [ - "create_or_update", + "edu.tamu.cpt.gff3.export_seq", "fetch_jbrowse", - "edu.tamu.cpt.fasta.seq_trans", "ncbi_blastp_wrapper", + "blastxml_to_gapped_gff3", "edu.tamu.cpt2.phage.intron_detection", "gff3.rebase", - "iframe", "cshl_fasta_formatter", - "jbrowse", - "blastxml_to_gapped_gff3", - "edu.tamu.cpt.gff3.export_seq" + "iframe", + "edu.tamu.cpt.fasta.seq_trans", + "create_or_update", + "jbrowse" ], "update_time": "2024-04-04", "versions": 11 @@ -31182,12 +46394,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "c8bc4af6dd3b5d02", @@ -31206,29 +46418,29 @@ "name:microgalaxy" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "interactive_tool_jupyter_notebook", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "interactive_tool_jupyter_notebook", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-04-04", "versions": 205 @@ -31240,13 +46452,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "9ddb703e1db13504", @@ -31259,10 +46471,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-04-04", "versions": 1 @@ -31274,8 +46486,8 @@ ], "doi": "", "edam_operation": [ - "Mapping", - "Pairwise sequence alignment" + "Pairwise sequence alignment", + "Mapping" ], "edam_topic": [], "id": "2b00b6498a2b4779", @@ -31300,10 +46512,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Pathway visualisation", "Pairwise sequence alignment", - "Structure visualisation" + "Genome visualisation", + "Structure visualisation", + "Pathway visualisation" ], "edam_topic": [], "id": "84414f3441946702", @@ -31316,8 +46528,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "minimap2", "samtools_bam_to_cram", + "minimap2", "jbrowse2" ], "update_time": "2024-03-30", @@ -31331,16 +46543,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f7cdaf862e6599c0", @@ -31355,17 +46567,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31379,20 +46591,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e138640778b7414c", @@ -31408,22 +46620,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31436,20 +46648,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "caba6d3d7db648e9", @@ -31465,20 +46677,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "merqury", + "gfastats", + "bandage_image", + "Cut1", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31491,16 +46703,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "12b0bd336c76a874", @@ -31516,16 +46728,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31538,13 +46750,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -31560,19 +46772,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-03-28", "versions": 1 @@ -31584,15 +46796,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "67be21795d403ca3", @@ -31607,13 +46819,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31625,19 +46837,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "1089e5c66dbcc1a3", @@ -31652,27 +46864,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31684,15 +46896,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2cf9f0e2ab5a7f8b", @@ -31707,13 +46919,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-28", "versions": 1 @@ -31725,17 +46937,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c0d1e965daf89006", @@ -31750,15 +46962,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-03-28", "versions": 1 @@ -31785,11 +46997,11 @@ "earth-system" ], "tools": [ - "xarray_metadata_info", "xarray_coords_info", - "argo_getdata", + "timeseries_extraction", "interactive_tool_odv", - "timeseries_extraction" + "xarray_metadata_info", + "argo_getdata" ], "update_time": "2024-03-27", "versions": 8 @@ -31816,12 +47028,12 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", + "Paste1", "anndata_ops", - "Cut1", + "anndata_manipulate", "tp_replace_in_column", - "Paste1" + "Cut1", + "anndata_inspect" ], "update_time": "2024-03-26", "versions": 4 @@ -31831,14 +47043,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", - "Primer removal", - "Read pre-processing", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", - "Sequence alignment" + "Read pre-processing", + "Sequence alignment", + "Sequence trimming", + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "9e03cf8cd5e5de08", @@ -31851,10 +47063,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", "htseq_count", "collection_column_join", "fastqc", + "rna_star", "cutadapt" ], "update_time": "2024-03-26", @@ -31881,8 +47093,8 @@ "ocean" ], "tools": [ - "interactive_tool_odv", - "interactive_tool_divand" + "interactive_tool_divand", + "interactive_tool_odv" ], "update_time": "2024-03-25", "versions": 2 @@ -31894,20 +47106,20 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", "Gene prediction", "Genome annotation", - "Taxonomic classification", + "Visualisation", "Statistical calculation", + "Genome assembly", + "Sequence assembly visualisation", + "Sequencing quality control", + "Aggregation", "Coding region prediction", - "Validation" + "Sequence composition calculation", + "Sequence assembly validation", + "Validation", + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "2e0075791f7fa384", @@ -31920,18 +47132,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "abricate", - "Kraken2Tax", + "prokka", + "unicycler", + "kraken2", "trimmomatic", + "abricate", + "multiqc", "porechop", - "kraken2", "bandage_image", "quast", - "multiqc", - "prokka", "fastqc", "staramr_search", - "unicycler" + "Kraken2Tax" ], "update_time": "2024-03-22", "versions": 2 @@ -31955,8 +47167,8 @@ "tags": [], "tools": [ "deeptools_bam_coverage", - "diffbind", - "seacr" + "seacr", + "diffbind" ], "update_time": "2024-03-22", "versions": 4 @@ -31981,8 +47193,8 @@ "apollo" ], "tools": [ - "edu.tamu.cpt.blast.relatedness.nuc", - "ncbi_blastn_wrapper" + "ncbi_blastn_wrapper", + "edu.tamu.cpt.blast.relatedness.nuc" ], "update_time": "2024-03-21", "versions": 3 @@ -31994,14 +47206,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "873e6ac4699ed7f6", @@ -32016,14 +47228,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32035,14 +47247,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "249c5d6698c8b98c", @@ -32057,14 +47269,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32076,15 +47288,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "44a2b6c8ae54eb31", @@ -32099,13 +47311,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32117,19 +47329,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "45f63151bf4f1a49", @@ -32144,27 +47356,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32176,19 +47388,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "f14ebad1c3c20067", @@ -32203,27 +47415,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32235,15 +47447,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1eac2ebffcbb8d59", @@ -32258,13 +47470,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32276,15 +47488,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ebbf5cfa946d11d3", @@ -32299,13 +47511,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -32317,17 +47529,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5279af5c95ae4f7a", @@ -32342,15 +47554,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-03-21", "versions": 1 @@ -32382,11 +47594,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Visualisation", - "Taxonomic classification", "Pairwise sequence alignment", - "Box-Whisker plot plotting" + "Visualisation", + "Scatter plot plotting", + "Box-Whisker plot plotting", + "Taxonomic classification" ], "edam_topic": [], "id": "d0ae255151450dad", @@ -32399,15 +47611,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "datamash_reverse", "kraken2", - "Cut1", - "join1", - "nanoplot", + "mergeCols1", "tp_replace_in_line", - "minimap2", "taxonomy_krona_chart", - "mergeCols1", - "datamash_reverse" + "nanoplot", + "join1", + "minimap2", + "Cut1" ], "update_time": "2024-03-19", "versions": 4 @@ -32417,22 +47629,22 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence trimming", - "Sequence assembly validation", "Gene prediction", - "Visualisation", - "Scaffolding", "Genome annotation", - "Genome assembly", "Statistical calculation", - "Coding region prediction", + "Visualisation", + "Genome assembly", "Primer removal", + "Sequencing quality control", + "Scaffolding", + "Transcriptome assembly", + "Aggregation", + "Coding region prediction", + "Sequence composition calculation", "Read pre-processing", - "Transcriptome assembly" + "Sequence trimming", + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "e8eb80ee09159bac", @@ -32445,13 +47657,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "prokka", + "fastqc", + "fasterq_dump", "barrnap", "quast", - "fasterq_dump", - "unicycler", "busco", - "prokka", - "fastqc", + "unicycler", "cutadapt" ], "update_time": "2024-03-16", @@ -32473,16 +47685,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "interactive_tool_rstudio", - "collapse_dataset", "bcftools_consensus", - "tb_variant_filter", + "snp_sites", + "collapse_dataset", "tp_replace_in_line", - "snp_dists", + "tp_cat", "Grep1", - "snp_sites", - "tp_cat" + "tb_variant_filter", + "tp_easyjoin_tool", + "snp_dists", + "interactive_tool_rstudio" ], "update_time": "2024-03-15", "versions": 0 @@ -32564,8 +47776,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "b483cf6a138d2372", @@ -32580,17 +47792,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-03-14", "versions": 1 @@ -32669,14 +47881,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-03-14", "versions": 1 @@ -32704,8 +47916,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-03-14", "versions": 1 @@ -32718,11 +47930,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "0599f049e4697839", @@ -32738,15 +47950,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-03-14", "versions": 1 @@ -32770,10 +47982,10 @@ ], "tools": [ "__EXTRACT_DATASET__", - "__FILTER_EMPTY_DATASETS__", - "map_param_value", "__BUILD_LIST__", - "Grep1" + "Grep1", + "map_param_value", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2024-03-13", "versions": 80 @@ -32785,14 +47997,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", - "Mapping", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Pairwise sequence alignment", + "Data handling", + "Pathway visualisation", + "Genome visualisation", + "Mapping" ], "edam_topic": [], "id": "309969a261189b5f", @@ -32805,19 +48017,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "bedtools_genomecoveragebed", + "seqtk_telo", + "mashmap", "Add_a_column1", + "deeptools_bam_coverage", "windowmasker_ustat", - "windowmasker_mkcounts", - "mashmap", - "seqtk_telo", - "minimap2", + "gfastats", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "bedtools_genomecoveragebed", + "fasta_compute_length" ], "update_time": "2024-03-13", "versions": 36 @@ -32828,9 +48040,9 @@ "doi": "", "edam_operation": [ "Sequence assembly validation", - "Transcriptome assembly", "Scaffolding", - "Genome assembly" + "Genome assembly", + "Transcriptome assembly" ], "edam_topic": [], "id": "88f80a31e3ff8663", @@ -32844,8 +48056,8 @@ "tags": [], "tools": [ "interactive_tool_blobtoolkit", - "busco", - "blobtoolkit" + "blobtoolkit", + "busco" ], "update_time": "2024-03-12", "versions": 12 @@ -32855,9 +48067,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", "Validation", + "Sequencing quality control", "Taxonomic classification" ], "edam_topic": [], @@ -32883,11 +48095,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Visualisation", - "Taxonomic classification", "Pairwise sequence alignment", - "Box-Whisker plot plotting" + "Visualisation", + "Scatter plot plotting", + "Box-Whisker plot plotting", + "Taxonomic classification" ], "edam_topic": [], "id": "14714876dda7186d", @@ -32900,15 +48112,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "datamash_reverse", "kraken2", - "Cut1", - "join1", - "nanoplot", + "mergeCols1", "tp_replace_in_line", - "minimap2", "taxonomy_krona_chart", - "mergeCols1", - "datamash_reverse" + "nanoplot", + "join1", + "minimap2", + "Cut1" ], "update_time": "2024-03-11", "versions": 3 @@ -32918,9 +48130,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0d41c30f6952f790", @@ -32943,21 +48155,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Data handling", - "Base-calling", - "Transcriptome assembly", - "De-novo assembly", + "Read binning", + "Genome assembly", "Sequence assembly", + "Mapping assembly", + "Scaffolding", "Sequencing quality control", + "Base-calling", + "Cross-assembly", + "Transcriptome assembly", "Pairwise sequence alignment", + "De-novo assembly", "Variant calling", - "Read binning", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Filtering", + "Data handling" ], "edam_topic": [], "id": "83a1b8949d87e3da", @@ -32971,15 +48183,15 @@ "tags": [], "tools": [ "flye", - "filtlong", "racon", - "medaka_consensus_pipeline", - "minimap2", - "busco", - "purge_dups", "__BUILD_LIST__", + "gfastats", + "busco", + "medaka_consensus_pipeline", "CONVERTER_gz_to_uncompressed", - "gfastats" + "filtlong", + "minimap2", + "purge_dups" ], "update_time": "2024-03-10", "versions": 7 @@ -33013,10 +48225,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "6fbd9b2274c62ebe", @@ -33030,12 +48242,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-03-07", "versions": 1 @@ -33048,16 +48260,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "399048afb4acef3d", @@ -33072,17 +48284,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-03-07", "versions": 1 @@ -33098,11 +48310,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "6a6e2c2335051fb5", @@ -33150,9 +48362,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-03-07", "versions": 1 @@ -33165,8 +48377,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "2e6ed783bdf05d16", @@ -33181,11 +48393,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-03-07", "versions": 1 @@ -33198,16 +48410,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f91245e580319e65", @@ -33223,16 +48435,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-03-07", "versions": 1 @@ -33245,8 +48457,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "da41880826c3d758", @@ -33259,8 +48471,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-03-07", "versions": 1 @@ -33273,8 +48485,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "3410a75a2a4899dc", @@ -33302,10 +48514,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "587e4d5ce25f48da", @@ -33320,20 +48532,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-03-07", "versions": 1 @@ -33347,10 +48559,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2e6561d8dadc9e17", @@ -33365,19 +48577,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-03-07", "versions": 1 @@ -33391,10 +48603,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2a33d4fcb806e942", @@ -33409,19 +48621,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-03-07", "versions": 1 @@ -33449,17 +48661,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2024-03-07", "versions": 1 @@ -33485,20 +48697,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-03-07", "versions": 1 @@ -33510,14 +48722,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "fcf745185d6e0ea4", @@ -33534,26 +48746,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-03-07", "versions": 1 @@ -33566,9 +48778,9 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", "Genome visualisation", - "Sequence motif recognition" + "Sequence motif recognition", + "Protein feature detection" ], "edam_topic": [], "id": "f62d7c0c7cc57eb6", @@ -33585,22 +48797,22 @@ "apollo" ], "tools": [ - "interproscan", - "create_or_update", - "edu.tamu.cpt.gff3.require_phage_start", + "edu.tamu.cpt.gff3.export_seq", + "edu.tamu.cpt.gff3.cdsParents", "fetch_jbrowse", - "gff3.rebase", "ncbi_blastp_wrapper", + "blastxml_to_gapped_gff3", + "gff3.rebase", + "edu.tamu.cpt.fasta.lipory", + "iframe", + "interproscan", "edu.tamu.cpt.fasta.seq_trans", - "edu.tamu.cpt.gff3.cdsParents", + "edu.tamu.cpt.gff3.require_phage_start", + "create_or_update", + "edu.tamu.cpt.gff3.remove_annots", "edu.tamu.cpt.fasta.remove_desc", - "iframe", "jbrowse", - "blastxml_to_gapped_gff3", - "edu.tamu.cpt.fasta.lipory", - "edu.tamu.cpt.gff3.export_seq", - "get_orfs_or_cdss", - "edu.tamu.cpt.gff3.remove_annots" + "get_orfs_or_cdss" ], "update_time": "2024-03-05", "versions": 5 @@ -33635,14 +48847,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Pairwise sequence alignment", - "Structure visualisation", - "Genome visualisation", "Genome annotation", - "Mapping", "Sequence file editing", - "Pathway visualisation" + "Structure visualisation", + "Pairwise sequence alignment", + "Data handling", + "Pathway visualisation", + "Genome visualisation", + "Mapping" ], "edam_topic": [], "id": "1ce406de61de8492", @@ -33655,18 +48867,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bedtools_genomecoveragebed", + "seqtk_telo", + "mashmap", "Add_a_column1", "windowmasker_ustat", - "windowmasker_mkcounts", - "mashmap", - "seqtk_telo", - "minimap2", "repeatmasker_wrapper", - "bedtools_makewindowsbed", - "fasta_compute_length", + "gfastats", "jbrowse2", - "gfastats" + "bedtools_makewindowsbed", + "windowmasker_mkcounts", + "minimap2", + "bedtools_genomecoveragebed", + "fasta_compute_length" ], "update_time": "2024-03-04", "versions": 13 @@ -33679,9 +48891,9 @@ ], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "e06934a35fc18f2c", @@ -33694,15 +48906,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2024-03-03", "versions": 9 @@ -33715,9 +48927,9 @@ ], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "c6adc3b665828a6f", @@ -33734,15 +48946,15 @@ "name:training" ], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2024-03-03", "versions": 29 @@ -33776,13 +48988,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "e85c9385870aadcc", @@ -33795,12 +49007,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", - "hisat2", + "featurecounts", "multiqc", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-02", "versions": 1 @@ -33905,13 +49117,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "e6c5fb1d37d29ec0", @@ -33924,12 +49136,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", + "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-01", "versions": 0 @@ -33939,13 +49151,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "63749bd3045ccd4a", @@ -33958,12 +49170,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", - "hisat2", + "featurecounts", "multiqc", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-01", "versions": 1 @@ -33973,13 +49185,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "9a1d17c12b139bda", @@ -33992,12 +49204,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", - "hisat2", + "featurecounts", "multiqc", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-01", "versions": 0 @@ -34007,13 +49219,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "1502fd3fa90d32d8", @@ -34026,12 +49238,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", - "hisat2", + "featurecounts", "multiqc", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-01", "versions": 0 @@ -34041,13 +49253,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "dbcf7af09e036754", @@ -34060,12 +49272,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", "cshl_fastq_quality_filter", - "hisat2", + "featurecounts", "multiqc", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2024-03-01", "versions": 0 @@ -34114,11 +49326,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-03-01", "versions": 0 @@ -34141,11 +49353,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-03-01", "versions": 0 @@ -34168,11 +49380,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-03-01", "versions": 0 @@ -34195,11 +49407,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-03-01", "versions": 0 @@ -34224,9 +49436,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-02-29", "versions": 0 @@ -34251,9 +49463,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-02-29", "versions": 0 @@ -34263,9 +49475,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "f81534f6cf8733e7", @@ -34278,8 +49490,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-02-29", "versions": 1 @@ -34289,9 +49501,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "38c7fa2653c5a2ee", @@ -34304,8 +49516,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-02-29", "versions": 0 @@ -34315,9 +49527,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "13da0b6780007d12", @@ -34330,8 +49542,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-02-29", "versions": 0 @@ -34341,9 +49553,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "1d0f438faa441c4e", @@ -34356,8 +49568,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-02-29", "versions": 0 @@ -34380,10 +49592,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "hicexplorer_hicbuildmatrix", "bowtie2", - "fasta_compute_length", - "hicexplorer_hicfindrestrictionsites" + "hicexplorer_hicbuildmatrix", + "hicexplorer_hicfindrestrictionsites", + "fasta_compute_length" ], "update_time": "2024-02-27", "versions": 15 @@ -34406,15 +49618,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "Add_a_column1", "Cut1", - "join1", "tp_grep_tool", "tp_replace_in_line", - "datamash_ops", "CONVERTER_uncompressed_to_gz", + "join1", "replace_column_with_key_value_file", - "Filter1" + "datamash_ops" ], "update_time": "2024-02-23", "versions": 15 @@ -34427,16 +49639,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d924fafd8e042952", @@ -34452,16 +49664,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-02-22", "versions": 1 @@ -34471,17 +49683,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "2a73d658446747de", @@ -34498,22 +49710,22 @@ "2024" ], "tools": [ - "gprofiler_gost", "limma_voom", + "Filter1", "gffread", - "Cut1", + "gprofiler_gost", "regex1", - "trim_galore", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", "tp_uniq_tool", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "Filter1", - "Grep1", - "tp_tail_tool" + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-02-19", "versions": 1 @@ -34523,8 +49735,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene set testing", "Gene functional annotation", + "Gene set testing", "Gene-set enrichment analysis" ], "edam_topic": [], @@ -34540,13 +49752,13 @@ "2" ], "tools": [ + "fgsea", "Add_a_column1", - "egsea", "tp_sort_header_tool", + "egsea", + "join1", "tp_cut_tool", "Cut1", - "join1", - "fgsea", "goseq" ], "update_time": "2024-02-18", @@ -34557,21 +49769,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Sequence annotation", + "Sequence comparison", + "Transcriptome assembly", "Sequence composition calculation", "De-novo assembly", - "Sequence annotation", - "Sequencing quality control", "Protein sequence analysis", - "Sequence alignment", - "Sequence comparison", - "Sequence assembly validation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq analysis", "Sequence analysis", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "b7a3cbcd32734e8b", @@ -34586,38 +49798,38 @@ "3" ], "tools": [ - "isoformswitchanalyzer", - "rseqc_read_distribution", - "__FILTER_FROM_FILE__", + "rseqc_junction_annotation", + "rseqc_geneBody_coverage", + "tp_cat", + "tp_uniq_tool", + "fastqc", + "rna_star", + "gene2exon1", "tp_grep_tool", "rseqc_infer_experiment", - "fastp", - "fastqc", - "rna_quast", - "rseqc_junction_saturation", - "gffcompare", - "pfamscan", - "gffread", - "stringtie_merge", - "tp_uniq_tool", + "collection_element_identifiers", "sort1", + "multiqc", "tp_sort_header_tool", - "rseqc_inner_distance", - "gtftobed12", "__FLATTEN__", + "cpat", "stringtie", "cat1", - "rseqc_junction_annotation", - "cpat", - "gene2exon1", - "rna_star", - "tp_awk_tool", - "Cut1", - "collection_element_identifiers", + "gffread", + "rseqc_junction_saturation", + "gffcompare", + "rseqc_read_distribution", + "rseqc_inner_distance", + "isoformswitchanalyzer", + "stringtie_merge", + "fastp", + "rna_quast", + "gtftobed12", "Remove beginning1", - "rseqc_geneBody_coverage", - "multiqc", - "tp_cat" + "Cut1", + "__FILTER_FROM_FILE__", + "tp_awk_tool", + "pfamscan" ], "update_time": "2024-02-18", "versions": 9 @@ -34627,10 +49839,10 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Gene set testing", "Gene functional annotation", - "Gene-set enrichment analysis" + "Gene set testing", + "Gene-set enrichment analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "732fa536cdc70c96", @@ -34643,16 +49855,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Add_a_column1", + "sklearn_numeric_clustering", "limma_voom", - "egsea", + "fgsea", + "Add_a_column1", "tp_sort_header_tool", - "tp_cut_tool", + "CONVERTER_uncompressed_to_gz", + "egsea", "join1", + "tp_cut_tool", "Cut1", - "sklearn_numeric_clustering", - "fgsea", - "CONVERTER_uncompressed_to_gz", "goseq" ], "update_time": "2024-02-17", @@ -34663,23 +49875,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", + "Visualisation", + "Sequence alignment", + "Sequencing quality control", + "Sequence annotation", + "Sequence comparison", + "Formatting", + "Transcriptome assembly", "Sequence composition calculation", "De-novo assembly", - "Sequence annotation", - "Sequencing quality control", "Protein sequence analysis", - "Sequence alignment", - "Formatting", - "Sequence comparison", - "Sequence assembly validation", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq analysis", "Sequence analysis", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "47a0407867a90f95", @@ -34692,41 +49904,41 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "isoformswitchanalyzer", - "rseqc_read_distribution", - "__FILTER_FROM_FILE__", + "rseqc_junction_annotation", + "rseqc_geneBody_coverage", + "fasta2tab", + "tp_cat", + "fastqc", + "rna_star", + "gene2exon1", "tp_grep_tool", "rseqc_infer_experiment", - "fastp", - "fastqc", - "rna_quast", + "collection_element_identifiers", + "sort1", + "multiqc", + "tp_sort_header_tool", + "__FLATTEN__", + "cpat", + "stringtie", + "gffread", "rseqc_junction_saturation", + "tp_sorted_uniq", "gffcompare", - "pfamscan", - "gffread", - "stringtie_merge", - "sort1", "hisat2", - "tp_sort_header_tool", + "rseqc_read_distribution", "rseqc_inner_distance", + "__FILTER_FROM_FILE__", + "isoformswitchanalyzer", "tab2fasta", + "stringtie_merge", + "fastp", + "rna_quast", "gtftobed12", - "__FLATTEN__", - "stringtie", - "fasta2tab", - "rseqc_junction_annotation", - "cpat", - "gene2exon1", - "rna_star", - "tp_awk_tool", + "Remove beginning1", "Cut1", - "tp_sorted_uniq", "pygenomeTracks", - "collection_element_identifiers", - "Remove beginning1", - "rseqc_geneBody_coverage", - "multiqc", - "tp_cat" + "tp_awk_tool", + "pfamscan" ], "update_time": "2024-02-17", "versions": 8 @@ -34737,13 +49949,13 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Genome visualisation", - "Read summarisation", "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Genome visualisation" ], "edam_topic": [], "id": "cae527ce845e770e", @@ -34758,10 +49970,10 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", - "jbrowse", "collection_column_join", - "fastqc" + "fastqc", + "hisat2", + "jbrowse" ], "update_time": "2024-02-17", "versions": 4 @@ -34784,12 +49996,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_sort_header_tool", - "comp1", - "datamash_ops", "Show beginning1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "tp_sort_header_tool", + "comp1", + "datamash_ops" ], "update_time": "2024-02-17", "versions": 1 @@ -34816,9 +50028,9 @@ "1" ], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-02-17", "versions": 1 @@ -34843,8 +50055,8 @@ "2" ], "tools": [ - "limma_voom", - "sklearn_numeric_clustering" + "sklearn_numeric_clustering", + "limma_voom" ], "update_time": "2024-02-17", "versions": 1 @@ -34855,13 +50067,13 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Genome visualisation", - "Read summarisation", "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Genome visualisation" ], "edam_topic": [], "id": "733650962d379da2", @@ -34878,10 +50090,10 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", - "jbrowse", "collection_column_join", - "fastqc" + "fastqc", + "hisat2", + "jbrowse" ], "update_time": "2024-02-17", "versions": 1 @@ -34906,11 +50118,11 @@ "1" ], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2024-02-17", "versions": 1 @@ -34920,15 +50132,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Genome visualisation", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Genome visualisation", + "Mapping" ], "edam_topic": [], "id": "d3dfe7ba11508c72", @@ -34941,17 +50153,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "featurecounts", - "comp1", "datamash_ops", "sort1", - "multiqc", - "hisat2", + "featurecounts", "jbrowse", + "Show beginning1", + "multiqc", + "bedtools_intersectbed", + "comp1", "collection_column_join", "fastqc", - "Show beginning1", - "bedtools_intersectbed" + "hisat2" ], "update_time": "2024-02-16", "versions": 1 @@ -34976,9 +50188,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-02-15", "versions": 2 @@ -34990,13 +50202,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "0ebfab0e957b7267", @@ -35009,10 +50221,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-02-15", "versions": 1 @@ -35025,16 +50237,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3192f92ac4d389b8", @@ -35049,17 +50261,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-02-15", "versions": 1 @@ -35083,9 +50295,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "datamash_reverse", "tp_replace_in_line", "taxonomy_krona_chart", - "datamash_reverse", "kraken2" ], "update_time": "2024-02-13", @@ -35096,9 +50308,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", "Gene functional annotation", - "Gene-set enrichment analysis" + "Gene-set enrichment analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "fa83e26e05418370", @@ -35111,14 +50323,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Add_a_column1", + "sklearn_numeric_clustering", "limma_voom", + "fgsea", + "Add_a_column1", "tp_sort_header_tool", + "CONVERTER_uncompressed_to_gz", "join1", "Cut1", - "sklearn_numeric_clustering", - "fgsea", - "CONVERTER_uncompressed_to_gz", "goseq" ], "update_time": "2024-02-10", @@ -35130,8 +50342,8 @@ "doi": "", "edam_operation": [ "Genetic variation analysis", - "Sequence analysis", "Genome visualisation", + "Sequence analysis", "Sequence annotation" ], "edam_topic": [], @@ -35149,24 +50361,24 @@ "apollo" ], "tools": [ - "edu.tamu.cpt.genbank.shinefind", + "filter_tabular", "edu.tamu.cpt.external.aragorn-gff3", - "metagene_annotator", + "glimmer_not_knowledge_based", + "edu.tamu.cpt.gff3.cdsParents", + "iframe", + "edu.tamu.cpt2.util.mga_to_gff3", "create_or_update", "edu.tamu.cpt.gff3.require_phage_start", - "glimmer_not_knowledge_based", + "metagene_annotator", + "edu.tamu.cpt.genbank.shinefind", + "edu.tamu.cpt.gff3.remove_annots", "edu.tamu.cpt2.util.glimmer3_to_gff3", + "edu.tamu.cpt.fasta.remove_desc", "edu.tamu.cpt.gff3.prepForApollo", - "aragorn_trna", - "edu.tamu.cpt2.util.mga_to_gff3", - "edu.tamu.cpt.gff3.cdsParents", "edu.tamu.cpt.gff3.fixsixpack", - "edu.tamu.cpt.fasta.remove_desc", - "iframe", "jbrowse", - "filter_tabular", "get_orfs_or_cdss", - "edu.tamu.cpt.gff3.remove_annots" + "aragorn_trna" ], "update_time": "2024-02-08", "versions": 2 @@ -35210,11 +50422,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "3403d5a8a71e0c3c", @@ -35262,9 +50474,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-02-08", "versions": 1 @@ -35274,12 +50486,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence merging", "Sequence contamination filtering", - "Sequence assembly", "Read pre-processing", + "Sequence assembly", + "Sequencing quality control", "Read mapping", - "Sequencing quality control" + "Sequence merging" ], "edam_topic": [], "id": "4643edf74f3eaec3", @@ -35292,16 +50504,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "tp_sort_header_tool", - "cshl_fastx_trimmer", - "Cut1", - "samtools_view", + "bowtie2", "fastq_to_tabular", "flash", + "Cut1", "fastp", + "tp_sort_header_tool", "Grouping1", - "bowtie2" + "tp_easyjoin_tool", + "cshl_fastx_trimmer", + "samtools_view" ], "update_time": "2024-02-06", "versions": 6 @@ -35322,12 +50534,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "eal_table_template", - "makeeml", + "taxo_cov_template", "__MERGE_COLLECTION__", - "geo_cov_template", "__BUILD_LIST__", - "taxo_cov_template" + "eal_table_template", + "geo_cov_template", + "makeeml" ], "update_time": "2024-02-04", "versions": 4 @@ -35348,8 +50560,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", "tp_head_tool", + "cat1", "Remove beginning1", "xmlstarlet" ], @@ -35361,10 +50573,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Sequencing quality control", - "Statistical calculation", - "Sequence composition calculation" + "Sequence composition calculation", + "Read mapping", + "Statistical calculation" ], "edam_topic": [], "id": "6deb9781d9f45a52", @@ -35377,8 +50589,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "bowtie2" + "bowtie2", + "fastqc" ], "update_time": "2024-02-03", "versions": 0 @@ -35401,9 +50613,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "sort1", - "fgsea" + "fgsea", + "Cut1" ], "update_time": "2024-02-02", "versions": 1 @@ -35426,10 +50638,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", - "Add_a_column1", "goseq", - "Cut1" + "Cut1", + "Add_a_column1", + "join1" ], "update_time": "2024-02-02", "versions": 2 @@ -35439,16 +50651,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence cluster visualisation", - "Phylogenetic tree analysis", - "Sequence visualisation", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Sequence clustering", "Phylogenetic tree generation", "Sequence motif recognition", "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree analysis", "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment" + "Sequence visualisation", + "Multiple sequence alignment", + "Sequence cluster visualisation" ], "edam_topic": [], "id": "974cc681d07ec788", @@ -35463,11 +50675,11 @@ "tools": [ "fasttree", "ncbi_blastp_wrapper", - "cd_hit", - "query_tabular", - "newick_display", "rgweblogo3", - "clustalw" + "newick_display", + "clustalw", + "query_tabular", + "cd_hit" ], "update_time": "2024-02-02", "versions": 5 @@ -35480,17 +50692,17 @@ ], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", + "Genome assembly", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation" ], "edam_topic": [], "id": "fba1671d835b6dd3", @@ -35506,17 +50718,17 @@ "hifi_assembly" ], "tools": [ - "Cut1", - "gfa_to_fa", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "quast", + "gfa_to_fa", + "Cut1", "Convert characters1", "busco", + "quast", "cutadapt", - "hifiasm", - "merqury" + "hifiasm" ], "update_time": "2024-01-31", "versions": 0 @@ -35576,8 +50788,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Gene-set enrichment analysis" + "Gene-set enrichment analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9a83043d5e847318", @@ -35591,8 +50803,8 @@ "tags": [], "tools": [ "sort1", - "Cut1", "limma_voom", + "Cut1", "fgsea" ], "update_time": "2024-01-27", @@ -35604,13 +50816,13 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Genome visualisation", - "Read summarisation", "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Genome visualisation" ], "edam_topic": [], "id": "5aba0f20d994b1a4", @@ -35625,10 +50837,10 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", - "jbrowse", "collection_column_join", - "fastqc" + "fastqc", + "hisat2", + "jbrowse" ], "update_time": "2024-01-27", "versions": 2 @@ -35651,12 +50863,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_sort_header_tool", - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "tp_sort_header_tool", + "comp1", + "datamash_ops" ], "update_time": "2024-01-27", "versions": 1 @@ -35681,9 +50893,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-01-27", "versions": 2 @@ -35693,26 +50905,26 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Phylogenetic tree analysis", - "Sequencing quality control", - "Phylogenetic analysis", - "Sequence comparison", "Visualisation", + "Primer removal", + "Sequencing quality control", + "Phylogenetic tree analysis", + "Sequence similarity search", + "Species frequency estimation", + "Conversion", "Phylogenetic inference", - "Read pre-processing", "Sequence trimming", - "Phylogenetic tree visualisation", + "Statistical calculation", "Nucleic acid sequence analysis", "Phylogenetic tree editing", - "Species frequency estimation", + "Phylogenetic analysis", + "Sequence comparison", "Sequence composition calculation", - "Statistical calculation", - "Primer removal", - "Taxonomic classification", - "Validation" + "Read pre-processing", + "Sequence alignment analysis", + "Validation", + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "fdca6c9d394986bf", @@ -35725,24 +50937,24 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metaphlan", - "bg_sortmerna", + "humann_regroup_table", + "humann_rename_table", + "export2graphlan", "graphlan_annotate", - "Cut1", + "bg_sortmerna", "tp_find_and_replace", - "humann_renorm_table", - "export2graphlan", - "graphlan", - "fastq_paired_end_interlacer", - "humann_regroup_table", - "taxonomy_krona_chart", + "Cut1", "multiqc", + "metaphlan", + "taxonomy_krona_chart", + "Grep1", "humann_unpack_pathways", - "humann_split_stratified_table", + "fastq_paired_end_interlacer", + "graphlan", "fastqc", - "Grep1", + "humann_split_stratified_table", "cutadapt", - "humann_rename_table" + "humann_renorm_table" ], "update_time": "2024-01-25", "versions": 0 @@ -35752,11 +50964,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Formatting", - "Sequence alignment" + "Formatting" ], "edam_topic": [], "id": "22454322d370b3ff", @@ -35773,14 +50985,14 @@ "name:variantcalling" ], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", + "bwa_mem2", "trimmomatic", - "vcffilter2", "bcftools_call", - "bwa_mem2", + "vcffilter2", "fastqc", - "bcftools_mpileup" + "bcftools_mpileup", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-25", "versions": 4 @@ -35793,15 +51005,15 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", - "Antimicrobial resistance prediction", "Sequence motif recognition", - "Scaffolding", "Genome assembly", - "Structural variation detection" + "Multilocus sequence typing", + "Scaffolding", + "Protein feature detection", + "Structural variation detection", + "Nucleic acid feature detection", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "3f5fe28793ed0c6c", @@ -35818,9 +51030,9 @@ "tools": [ "abricate", "bakta", + "isescan", "integron_finder", - "plasmidfinder", - "isescan" + "plasmidfinder" ], "update_time": "2024-01-25", "versions": 3 @@ -35845,9 +51057,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2024-01-24", "versions": 1 @@ -35860,18 +51072,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "b211fceaecf41c9e", @@ -35887,19 +51099,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-01-18", "versions": 1 @@ -35912,19 +51124,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "5115299e77df8104", @@ -35940,20 +51152,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-01-18", "versions": 1 @@ -35965,18 +51177,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "5c15f251642bfa1f", @@ -35993,21 +51205,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2024-01-18", "versions": 1 @@ -36019,14 +51231,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "4b4bfc79205d83f1", @@ -36043,26 +51255,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-01-18", "versions": 1 @@ -36075,11 +51287,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "6be946c7ec91835e", @@ -36095,15 +51307,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-01-18", "versions": 1 @@ -36142,18 +51354,18 @@ ], "doi": "", "edam_operation": [ + "Copy number estimation", + "Statistical calculation", "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", "Sequence alignment", - "Statistical calculation", - "Copy number estimation", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "75e88603745e069e", @@ -36170,22 +51382,22 @@ "miracum" ], "tools": [ - "bwa_mem", - "bamleftalign", "samtools_calmd", + "samtools_rmdup", "__EXTRACT_DATASET__", + "control_freec", "trimmomatic", - "circos", - "samtools_view", - "samtools_rmdup", - "tp_replace_in_line", + "fastqc", "multiqc", + "tp_replace_in_line", + "__BUILD_LIST__", + "Grep1", + "bwa_mem", "tp_text_file_with_recurring_lines", + "circos", + "bamleftalign", "__RELABEL_FROM_FILE__", - "fastqc", - "control_freec", - "__BUILD_LIST__", - "Grep1" + "samtools_view" ], "update_time": "2024-01-16", "versions": 18 @@ -36195,12 +51407,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence merging", "Sequence contamination filtering", - "Sequence assembly", "Read pre-processing", + "Sequence assembly", + "Sequencing quality control", "Read mapping", - "Sequencing quality control" + "Sequence merging" ], "edam_topic": [], "id": "987a2abb5cd56e57", @@ -36213,14 +51425,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_sort_header_tool", - "cshl_fastx_trimmer", - "Cut1", - "samtools_view", + "bowtie2", "flash", + "Cut1", "fastp", + "tp_sort_header_tool", "Grouping1", - "bowtie2" + "cshl_fastx_trimmer", + "samtools_view" ], "update_time": "2024-01-09", "versions": 3 @@ -36243,11 +51455,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ctb_im_rxn_maker", "openbabel_svg_depiction", + "openbabel_compound_convert", "chembl", - "ctb_im_rxn_maker", - "ctb_silicos_qed", - "openbabel_compound_convert" + "ctb_silicos_qed" ], "update_time": "2024-01-01", "versions": 7 @@ -36257,17 +51469,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "48fe9c4de045d414", @@ -36280,22 +51492,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", + "Filter1", "gffread", - "Cut1", + "gprofiler_gost", "regex1", - "trim_galore", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", "tp_uniq_tool", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "Filter1", - "Grep1", - "tp_tail_tool" + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-12-29", "versions": 27 @@ -36311,11 +51523,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "90a32c95b60f5221", @@ -36363,9 +51575,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2023-12-28", "versions": 1 @@ -36375,17 +51587,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1590085d315aa80e", @@ -36398,22 +51610,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", + "Filter1", "gffread", - "Cut1", + "gprofiler_gost", "regex1", - "trim_galore", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", "tp_uniq_tool", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "Filter1", - "Grep1", - "tp_tail_tool" + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-12-26", "versions": 39 @@ -36423,16 +51635,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "a62f21701ff37788", @@ -36445,15 +51657,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2023-12-23", "versions": 1 @@ -36463,17 +51675,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "8bc1c3b9e665ea37", @@ -36486,22 +51698,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", + "Filter1", "gffread", - "Cut1", + "gprofiler_gost", "regex1", - "trim_galore", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", "tp_uniq_tool", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "Filter1", - "Grep1", - "tp_tail_tool" + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-12-22", "versions": 28 @@ -36522,17 +51734,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ucsc_cell_browser", - "scanpy_compute_graph", "scanpy_read_10x", + "scanpy_find_cluster", + "scanpy_compute_graph", + "scanpy_run_umap", "scanpy_find_markers", "scanpy_run_pca", + "ucsc_cell_browser", "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", - "scanpy_scale_data", "scanpy_filter_cells", - "scanpy_run_umap" + "scanpy_scale_data", + "scanpy_normalise_data" ], "update_time": "2023-12-19", "versions": 1 @@ -36560,24 +51772,24 @@ "transcriptomics" ], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "anndata_manipulate", - "anndata_ops", - "join1", "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "anndata_manipulate", + "anndata_ops", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2023-12-18", "versions": 6 @@ -36604,10 +51816,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "seurat_read10x", "anndata_inspect", - "dropletutils", "datamash_transpose", - "seurat_read10x" + "dropletutils" ], "update_time": "2023-12-15", "versions": 7 @@ -36635,8 +51847,8 @@ "tags": [], "tools": [ "anndata_inspect", - "dropletutils", "datamash_transpose", + "dropletutils", "dropletutils_read_10x" ], "update_time": "2023-12-15", @@ -36647,16 +51859,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2a13eb981d6ee36e", @@ -36669,15 +51881,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2023-12-14", "versions": 4 @@ -36687,10 +51899,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -36718,16 +51930,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "8af41219411062ad", @@ -36744,22 +51956,22 @@ ], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2023-12-14", "versions": 1 @@ -36783,17 +51995,17 @@ "name:clinicalmp" ], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2023-12-14", "versions": 1 @@ -36803,14 +52015,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "a49275eb8b2b2ecb", @@ -36826,8 +52038,8 @@ "name:microgalaxy" ], "tools": [ - "Cut1", "Grep1", + "Cut1", "Grouping1", "maxquant" ], @@ -36856,8 +52068,8 @@ "name:clinicalmp" ], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2023-12-14", @@ -36868,34 +52080,34 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", - "Sequence assembly", - "Coding region prediction", - "Sequencing quality control", - "Formatting", "Visualisation", - "Data retrieval", - "Read pre-processing", - "Sequence trimming", - "Database search", + "Sequence motif recognition", "Gene functional annotation", - "Protein feature detection", - "Sequence profile generation", + "Sequence assembly", + "Database search", + "Primer removal", + "Sequencing quality control", "Format validation", - "Sequence composition calculation", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence analysis", "Sequence database search", - "Local alignment", + "Sequence trimming", "Sequence assembly validation", + "Sequence profile generation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", - "Primer removal", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment", - "Sequence analysis", - "Validation" + "Local alignment", + "Read pre-processing", + "Sequence composition calculation", + "Sequence generation", + "Data retrieval", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "d57d41e306241396", @@ -36910,23 +52122,23 @@ "name:microgalaxy" ], "tools": [ - "interproscan", - "fasplit", - "tp_awk_tool", - "maxbin2", - "trim_galore", - "quast", - "kofamscan", - "tp_grep_tool", "fraggenescan", - "hmmer_hmmscan", "sort1", - "fastqc", + "kofamscan", + "coverm_contig", + "cat_bins", + "trim_galore", "coverm_genome", + "tp_cat", + "fasplit", "checkm_lineage_wf", - "cat_bins", - "coverm_contig", - "tp_cat" + "hmmer_hmmscan", + "quast", + "fastqc", + "interproscan", + "maxbin2", + "tp_grep_tool", + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -36936,14 +52148,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "01ac8bf9832789e2", @@ -36968,16 +52180,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Gene expression profiling", + "Statistical calculation", + "Primer removal", "Sequencing quality control", "Sequence comparison", - "Primer removal", + "Sequence similarity search", "Read pre-processing", + "Sequence composition calculation", + "Sequence alignment analysis", "Sequence trimming", - "Statistical calculation" + "Gene expression profiling" ], "edam_topic": [], "id": "3733bcdf5b458be7", @@ -36992,12 +52204,12 @@ "name:microgalaxy" ], "tools": [ + "kallisto_quant", "bg_sortmerna", "trim_galore", - "__UNZIP_COLLECTION__", - "kallisto_quant", "collection_column_join", - "fastqc" + "fastqc", + "__UNZIP_COLLECTION__" ], "update_time": "2023-12-14", "versions": 1 @@ -37007,16 +52219,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "695f7defb516d80d", @@ -37032,12 +52244,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2023-12-14", "versions": 0 @@ -37047,16 +52259,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "4c364c6be27981ba", @@ -37072,12 +52284,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2023-12-14", "versions": 0 @@ -37104,11 +52316,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2023-12-14", "versions": 0 @@ -37118,9 +52330,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence alignment", "Read mapping", - "Mapping", - "Sequence alignment" + "Mapping" ], "edam_topic": [], "id": "0e492839192d26e0", @@ -37136,26 +52348,26 @@ "name:microgalaxy" ], "tools": [ - "lastz_wrapper_2", - "tp_grep_tool", - "fasta_filter_by_length", - "tp_sed_tool", - "datamash_ops", - "mergeCols1", - "tp_sort_header_tool", - "bedtools_complementbed", "collapse_dataset", + "Cut1", + "tp_cat", + "Grep1", + "random_lines1", "join1", + "tp_grep_tool", + "Filter1", + "bedtools_complementbed", + "tp_sort_header_tool", "addValue", - "random_lines1", "fasta_compute_length", "cat1", - "Cut1", + "lastz_wrapper_2", "bedtools_sortbed", - "Filter1", - "Grep1", + "fasta_filter_by_length", + "mergeCols1", "bedtools_intersectbed", - "tp_cat" + "tp_sed_tool", + "datamash_ops" ], "update_time": "2023-12-14", "versions": 0 @@ -37165,13 +52377,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Visualisation", "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", "Sequence composition calculation", + "Visualisation", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "08eb5e55109c4d9c", @@ -37188,11 +52400,11 @@ ], "tools": [ "kraken2", - "porechop", - "tp_replace_in_line", - "taxonomy_krona_chart", "fastp", "multiqc", + "tp_replace_in_line", + "porechop", + "taxonomy_krona_chart", "Remove beginning1", "fastqc", "datamash_reverse" @@ -37235,14 +52447,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -37259,15 +52471,15 @@ "name:microgalaxy" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "racon", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2023-12-14", "versions": 0 @@ -37281,13 +52493,13 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Visualisation", "Sequence contamination filtering", + "Sequence composition calculation", + "Visualisation", "Statistical calculation", "Taxonomic classification", - "Sequence composition calculation", - "Sequencing quality control" + "Sequencing quality control", + "Aggregation" ], "edam_topic": [], "id": "0590554db9794d13", @@ -37303,13 +52515,13 @@ "name:microgalaxy" ], "tools": [ + "Filter1", "kraken2", - "porechop", - "taxonomy_krona_chart", + "krakentools_kreport2krona", "fastp", - "fastqc", - "Filter1", - "krakentools_kreport2krona" + "taxonomy_krona_chart", + "porechop", + "fastqc" ], "update_time": "2023-12-14", "versions": 0 @@ -37319,20 +52531,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Sequence contamination filtering", + "Statistical calculation", + "Genome assembly", + "Primer removal", "Sequencing quality control", + "Sequence file editing", "Formatting", - "Variant calling", - "Genome assembly", "Sequence trimming", - "Statistical calculation", - "Sequence contamination filtering", "Read pre-processing", - "Primer removal", - "Sequence file editing" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "ce5c16ac23c4fbb1", @@ -37347,17 +52559,17 @@ "name:microgalaxy" ], "tools": [ - "fastqc", - "seqtk_subseq", - "bamtools", + "bowtie2", "filter_tabular", - "bg_uniq", "ngsutils_bam_filter", "megahit", + "tp_cat", + "seqtk_subseq", "random_lines1", - "bowtie2", + "bamtools", + "fastqc", "cutadapt", - "tp_cat" + "bg_uniq" ], "update_time": "2023-12-14", "versions": 0 @@ -37367,11 +52579,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", "Genome assembly", - "Read mapping", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Read mapping" ], "edam_topic": [], "id": "62c47e3c9d4f3aa3", @@ -37386,14 +52598,14 @@ "name:microgalaxy" ], "tools": [ + "bowtie2", + "bandage_info", "megahit_contig2fastg", + "megahit", "bandage_image", - "quast", "collection_column_join", - "metaspades", - "megahit", - "bowtie2", - "bandage_info" + "quast", + "metaspades" ], "update_time": "2023-12-14", "versions": 0 @@ -37419,12 +52631,12 @@ "name:microgalaxy" ], "tools": [ - "metaphlan2krona", - "metaphlan2", "humann2_renorm_table", "taxonomy_krona_chart", - "humann2", - "humann2_regroup_table" + "humann2_regroup_table", + "metaphlan2", + "metaphlan2krona", + "humann2" ], "update_time": "2023-12-14", "versions": 0 @@ -37436,12 +52648,12 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", "Statistical calculation", + "Nucleic acid sequence analysis", "Taxonomic classification", "Phylogenetic tree analysis", - "Nucleic acid sequence analysis" + "Aggregation" ], "edam_topic": [], "id": "4f0daf8e9dd54127", @@ -37457,15 +52669,15 @@ "name:microgalaxy" ], "tools": [ - "metaphlan", + "kraken_biom", "kraken2", + "krakentools_kreport2krona", "interactive_tool_phinch", - "kraken_biom", - "est_abundance", "taxonomy_krona_chart", - "__UNZIP_COLLECTION__", + "est_abundance", + "metaphlan", "interactive_tool_pavian", - "krakentools_kreport2krona" + "__UNZIP_COLLECTION__" ], "update_time": "2023-12-14", "versions": 0 @@ -37475,13 +52687,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "565c989730f68362", @@ -37498,20 +52710,20 @@ ], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "krona-text", - "mothur_pre_cluster", - "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", - "mothur_make_group", "mothur_classify_otu", + "mothur_make_group", + "mothur_screen_seqs", + "mothur_pre_cluster", "mothur_summary_seqs", - "mothur_merge_files", + "mothur_align_seqs", + "mothur_filter_seqs", "mothur_make_biom", - "mothur_align_seqs" + "krona-text", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2023-12-14", "versions": 0 @@ -37522,9 +52734,9 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", "Phylogenetic tree generation", - "Genome visualisation" + "Genome visualisation", + "Variant calling" ], "edam_topic": [], "id": "515ef1601bc24a6c", @@ -37551,17 +52763,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "291c36e1b18e9deb", @@ -37577,16 +52789,16 @@ "name:microgalaxy" ], "tools": [ - "bwa_mem", - "bamleftalign", - "picard_MarkDuplicates", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "Cut1", - "freebayes", + "vcf2tsv", + "bwa_mem", "fastqc", "bamFilter", - "vcf2tsv" + "Cut1", + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2023-12-14", "versions": 0 @@ -37596,16 +52808,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "c67d2e75eeb4fd19", @@ -37621,39 +52833,39 @@ "name:microgalaxy" ], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_cluster", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_seq_error", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", "mothur_remove_groups", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", + "mothur_pre_cluster", "mothur_get_groups", - "mothur_align_seqs", + "mothur_chimera_vsearch", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_cluster", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", - "XY_Plot_1", - "mothur_seq_error" + "XY_Plot_1" ], "update_time": "2023-12-14", "versions": 0 @@ -37665,9 +52877,9 @@ ], "doi": "", "edam_operation": [ - "Multiple sequence alignment", + "Phylogenetic tree generation", "Sequence alignment analysis", - "Phylogenetic tree generation" + "Multiple sequence alignment" ], "edam_topic": [], "id": "86900be4282d4b1d", @@ -37684,20 +52896,20 @@ "name:microgalaxy" ], "tools": [ + "regexColumn1", "cat1", - "tp_split_on_column", + "Filter1", "Add_a_column1", - "regexColumn1", + "rbc_mafft", "collapse_dataset", - "join1", - "Cut1", "tab2fasta", + "bg_diamond_view", "rapidnj", - "rbc_mafft", "bg_diamond", - "bg_diamond_view", - "Filter1", - "gops_intersect_1" + "gops_intersect_1", + "join1", + "Cut1", + "tp_split_on_column" ], "update_time": "2023-12-14", "versions": 0 @@ -37707,16 +52919,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", "Statistical calculation", + "Visualisation", "Genome assembly", + "Sequencing quality control", + "Aggregation", "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation", "Validation" ], "edam_topic": [], @@ -37733,10 +52945,10 @@ "name:microgalaxy" ], "tools": [ - "quast", - "multiqc", "prokka", "fastqc", + "multiqc", + "quast", "unicycler" ], "update_time": "2023-12-14", @@ -37763,11 +52975,11 @@ "name:microgalaxy" ], "tools": [ - "create_or_update", "list_organism", "iframe", - "jbrowse", - "create_account" + "create_account", + "create_or_update", + "jbrowse" ], "update_time": "2023-12-14", "versions": 0 @@ -37777,9 +52989,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", "Coding region prediction", + "Genome visualisation", "Genome annotation" ], "edam_topic": [], @@ -37796,8 +53008,8 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2023-12-14", "versions": 0 @@ -37807,23 +53019,23 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", + "Genome annotation", + "Genome assembly", "Scatter plot plotting", - "Base-calling", - "De-novo assembly", "Sequence assembly", - "Pairwise sequence alignment", - "Genome assembly", - "Box-Whisker plot plotting", + "Mapping assembly", "Sequence assembly visualisation", - "Variant calling", - "Genome visualisation", - "Gene prediction", - "Genome annotation", - "Sequence analysis", + "Base-calling", + "Box-Whisker plot plotting", "Sequence visualisation", + "Cross-assembly", "Coding region prediction", - "Mapping assembly", - "Cross-assembly" + "De-novo assembly", + "Pairwise sequence alignment", + "Sequence analysis", + "Variant calling", + "Genome visualisation" ], "edam_topic": [], "id": "152223c8aed27357", @@ -37839,42 +53051,42 @@ "name:microgalaxy" ], "tools": [ - "tp_easyjoin_tool", + "trimmomatic", + "ncbi_blastn_wrapper", + "regex_replace", + "deeptools_bam_coverage", + "tp_cat", + "fasta2tab", + "Grep1", + "join1", "bg_column_arrange_by_header", - "bandage_image", - "minimap2", - "jbrowse", - "prokka", - "tbl2gff3", - "circos", - "staramr_search", + "medaka_consensus_pipeline", "circos_interval_to_tile", - "tp_cut_tool", - "regex1", - "tp_text_file_with_recurring_lines", - "ncbi_blastn_wrapper", - "tp_split_on_column", + "staramr_search", + "prokka", + "Filter1", "Add_a_column1", + "regex1", + "nanoplot", "tp_sort_header_tool", "gff2bed1", - "join1", - "tab2fasta", - "regex_replace", - "fasta_compute_length", - "deeptools_bam_coverage", + "tp_easyjoin_tool", "circos_gc_skew", - "fasta2tab", - "trimmomatic", + "fasta_compute_length", "flye", - "Cut1", - "nanoplot", - "medaka_consensus_pipeline", + "tp_head_tool", + "bandage_image", + "minimap2", + "tbl2gff3", + "tab2fasta", "PlasFlow", + "jbrowse", "circos_wiggle_to_scatter", - "tp_head_tool", - "Filter1", - "Grep1", - "tp_cat" + "tp_text_file_with_recurring_lines", + "circos", + "tp_cut_tool", + "Cut1", + "tp_split_on_column" ], "update_time": "2023-12-14", "versions": 0 @@ -37901,8 +53113,8 @@ "name:microgalaxy" ], "tools": [ - "interactive_tool_rstudio", - "raxml" + "raxml", + "interactive_tool_rstudio" ], "update_time": "2023-12-14", "versions": 0 @@ -37927,10 +53139,10 @@ ], "tools": [ "bcftools_consensus", - "tb_variant_filter", - "snp_dists", "snp_sites", - "tp_cat" + "tp_cat", + "tb_variant_filter", + "snp_dists" ], "update_time": "2023-12-14", "versions": 0 @@ -37941,8 +53153,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Variant calling" ], "edam_topic": [], "id": "3a8fde248a4d0383", @@ -37958,9 +53170,9 @@ "name:microgalaxy" ], "tools": [ - "__MERGE_COLLECTION__", - "tb_variant_filter", "snippy", + "tb_variant_filter", + "__MERGE_COLLECTION__", "trimmomatic" ], "update_time": "2023-12-14", @@ -37987,14 +53199,14 @@ "name:microgalaxy" ], "tools": [ - "tb_profiler_profile", - "samtools_view", - "tp_grep_tool", - "tp_sed_tool", + "addName", "__MERGE_COLLECTION__", "tp_replace_in_line", - "addName", - "tp_cat" + "tp_cat", + "tp_sed_tool", + "tp_grep_tool", + "samtools_view", + "tb_profiler_profile" ], "update_time": "2023-12-14", "versions": 0 @@ -38006,16 +53218,16 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Statistical calculation", + "Phylogenetic tree generation", "Sequencing quality control", + "Sequence composition calculation", "Variant calling", - "Phylogenetic tree generation", + "Validation", + "Phylogenetic tree visualisation", "Genome visualisation", "Antimicrobial resistance prediction", - "Statistical calculation", - "Taxonomic classification", - "Phylogenetic tree visualisation", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "3ff4dbcc7a602e6b", @@ -38032,15 +53244,15 @@ "name:microgalaxy" ], "tools": [ - "tb_profiler_profile", - "tbvcfreport", "kraken2", "trimmomatic", + "multiqc", "tb_variant_filter", + "tbvcfreport", + "fastqc", "snippy", - "multiqc", "jbrowse", - "fastqc" + "tb_profiler_profile" ], "update_time": "2023-12-14", "versions": 0 @@ -38063,13 +53275,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_ops", "regexColumn1", - "tp_find_and_replace", "scanpy_read_10x", + "retrieve_scxa", + "tp_find_and_replace", + "anndata_ops", "tp_grep_tool", - "seurat_read10x", - "retrieve_scxa" + "seurat_read10x" ], "update_time": "2023-12-14", "versions": 6 @@ -38104,8 +53316,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -38122,13 +53334,13 @@ "hpylori" ], "tools": [ - "bcftools_norm", - "tp_awk_tool", - "freebayes", "bowtie2", - "vcf2tsv", + "freebayes", + "bcftools_norm", "bcftools_view", - "snpSift_filter" + "vcf2tsv", + "snpSift_filter", + "tp_awk_tool" ], "update_time": "2023-12-13", "versions": 2 @@ -38138,8 +53350,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -38156,15 +53368,15 @@ "hpylori" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "collapse_dataset", + "bowtie2", "collection_element_identifiers", - "vcf2tsv", "freebayes", - "bowtie2", + "bcftools_norm", + "collapse_dataset", + "tp_cat", "samtools_coverage", - "tp_cat" + "samtools_depth", + "vcf2tsv" ], "update_time": "2023-12-13", "versions": 13 @@ -38174,13 +53386,13 @@ "creators": [], "doi": "", "edam_operation": [ + "Mapping", + "k-mer counting", "Visualisation", - "Comparison", "Alignment", "Nucleic acid feature detection", - "Mapping", "Formatting", - "k-mer counting" + "Comparison" ], "edam_topic": [], "id": "437704898229dfb6", @@ -38196,16 +53408,16 @@ "name:microgalaxy" ], "tools": [ - "infernal_cmsearch", "gops_concat_1", - "tp_awk_tool", + "infernal_cmsearch", + "taxonomy_krona_chart", + "cmsearch_deoverlap", "bedtools_maskfastabed", - "mapseq", - "bedtools_getfastabed", "biom_convert", - "taxonomy_krona_chart", + "mapseq", "query_tabular", - "cmsearch_deoverlap" + "bedtools_getfastabed", + "tp_awk_tool" ], "update_time": "2023-12-13", "versions": 1 @@ -38215,15 +53427,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence merging", - "Sequence composition calculation", - "Sequencing quality control", "Sequence contamination filtering", + "Statistical calculation", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Validation" + "Validation", + "Data handling", + "Sequence merging" ], "edam_topic": [], "id": "8f415b0c409f56f7", @@ -38239,17 +53451,17 @@ "name:microgalaxy" ], "tools": [ - "prinseq", + "fastq_to_fasta_python", "trimmomatic", "tp_find_and_replace", - "fastq_dump", + "prinseq", "fastp", - "__UNZIP_COLLECTION__", - "cshl_fasta_formatter", "multiqc", + "cshl_fasta_formatter", "iuc_pear", "fastqc", - "fastq_to_fasta_python" + "fastq_dump", + "__UNZIP_COLLECTION__" ], "update_time": "2023-12-13", "versions": 1 @@ -38273,14 +53485,14 @@ "tags": [], "tools": [ "cat1", - "jvarkit_wgscoverageplotter", - "mimodd_varreport", + "bowtie2", + "snpEff", "trimmomatic", + "mimodd_varreport", "mimodd_varextract", - "mimodd_vcf_filter", - "snpEff", - "bowtie2", - "mimodd_varcall" + "jvarkit_wgscoverageplotter", + "mimodd_varcall", + "mimodd_vcf_filter" ], "update_time": "2023-12-12", "versions": 11 @@ -38290,19 +53502,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Sequence trimming", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ccef778cfd9024d1", @@ -38315,25 +53527,25 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rseqc_infer_experiment", - "fastqc", - "tp_replace_in_line", - "deseq2", - "tp_sort_header_tool", + "tp_cat", "join1", - "featurecounts", - "gtftobed12", - "__FLATTEN__", - "ggplot2_heatmap2", + "fastqc", "rna_star", - "Cut1", - "collection_element_identifiers", "__TAG_FROM_FILE__", - "deg_annotate", - "multiqc", + "rseqc_infer_experiment", + "collection_element_identifiers", "Filter1", + "featurecounts", + "multiqc", + "tp_sort_header_tool", + "deg_annotate", + "__FLATTEN__", "cutadapt", - "tp_cat" + "deseq2", + "tp_replace_in_line", + "gtftobed12", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2023-12-09", "versions": 0 @@ -38343,17 +53555,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", - "Differential gene expression analysis", "Peak calling", + "Differential gene expression analysis", "Sequence alignment", + "Generation", "Gene regulatory network analysis", - "Read summarisation", - "Mapping", "Genome indexing", - "Generation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0229f3f3835c2d53", @@ -38366,18 +53578,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "__EXTRACT_DATASET__", + "macs2_callpeak", "edger", - "trimmomatic", - "tp_awk_tool", - "rna_star", "featurecounts", + "trimmomatic", + "__EXTRACT_DATASET__", + "__BUILD_LIST__", + "bedtools_intersectbed", "comp1", "collection_column_join", - "macs2_callpeak", - "__BUILD_LIST__", - "bedtools_intersectbed" + "bwa_mem", + "rna_star", + "tp_awk_tool" ], "update_time": "2023-12-08", "versions": 6 @@ -38387,11 +53599,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Read mapping", - "Sequencing quality control", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control", + "Read mapping", + "Read summarisation" ], "edam_topic": [], "id": "4566262dd0acc8ab", @@ -38408,8 +53620,8 @@ "name:microgalaxy" ], "tools": [ - "multiqc", "bowtie2", + "multiqc", "featurecounts" ], "update_time": "2023-12-07", @@ -38420,25 +53632,25 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence annotation", - "Sequencing quality control", - "Fold recognition", - "Visualisation", + "Genome annotation", "Homology-based gene prediction", - "Query and retrieval", - "Genome assembly", - "Sequence clustering", + "Information extraction", + "Visualisation", "Gene functional annotation", - "Sequence composition calculation", - "Read mapping", + "Sequencing quality control", + "Fold recognition", + "Sequence analysis", "Sequence assembly validation", - "Genome annotation", - "Statistical calculation", + "Read mapping", "Mapping", - "Sequence analysis", - "Information extraction", - "Validation" + "Statistical calculation", + "Sequence clustering", + "Genome assembly", + "Query and retrieval", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Sequence annotation" ], "edam_topic": [], "id": "9b9e1e28f3683f92", @@ -38455,22 +53667,22 @@ "name:microgalaxy" ], "tools": [ + "bowtie2", "cat1", - "metagene_annotator", - "bg_diamond_makedb", "metaeuk_easy_predict", + "multiqc", + "megahit", "translate_nucleotides", - "quast", + "bg_diamond", + "eggnog_mapper", "kofamscan", + "quast", + "fastqc", "bedtools_getfastabed", - "cd_hit", - "eggnog_mapper", - "multiqc", - "bg_diamond", "dbbuilder", - "megahit", - "fastqc", - "bowtie2" + "metagene_annotator", + "bg_diamond_makedb", + "cd_hit" ], "update_time": "2023-12-07", "versions": 72 @@ -38480,10 +53692,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "bb604ff5e010e7ab", @@ -38500,9 +53712,9 @@ "name:microgalaxy" ], "tools": [ - "fastqc", + "trimmomatic", "multiqc", - "trimmomatic" + "fastqc" ], "update_time": "2023-12-07", "versions": 51 @@ -38512,10 +53724,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Read mapping", "Expression analysis", - "Cross-assembly" + "Read mapping", + "Cross-assembly", + "Taxonomic classification" ], "edam_topic": [], "id": "bdc7cfaac0db2eab", @@ -38532,12 +53744,12 @@ "name:microgalaxy" ], "tools": [ - "seq_filter_by_id", - "kraken2", + "bowtie2", "fastq_to_tabular", "filter_tabular", - "bowtie2", - "recentrifuge" + "recentrifuge", + "kraken2", + "seq_filter_by_id" ], "update_time": "2023-12-07", "versions": 28 @@ -38547,13 +53759,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Standardisation and normalisation", + "Statistical calculation", "Visualisation", "Expression analysis", - "Statistical calculation", - "Taxonomic classification", + "Filtering", "Cross-assembly", - "Standardisation and normalisation" + "Taxonomic classification" ], "edam_topic": [], "id": "e69b555faa6bb962", @@ -38571,10 +53783,10 @@ ], "tools": [ "maaslin2", - "kraken2", - "interactive_tool_phinch", "kraken_biom", - "recentrifuge" + "recentrifuge", + "kraken2", + "interactive_tool_phinch" ], "update_time": "2023-12-07", "versions": 18 @@ -38587,8 +53799,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "4025b5dca188e6a4", @@ -38601,8 +53813,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2023-12-07", "versions": 1 @@ -38615,8 +53827,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "4eb8aec8a5be98b3", @@ -38644,10 +53856,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ea8bb8eefdb4ba7a", @@ -38662,20 +53874,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-12-07", "versions": 1 @@ -38689,10 +53901,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9e4df2893767591a", @@ -38707,19 +53919,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-12-07", "versions": 1 @@ -38733,10 +53945,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "55a9fc5d30392777", @@ -38751,19 +53963,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-12-07", "versions": 1 @@ -38814,8 +54026,8 @@ "tags": [], "tools": [ "__ZIP_COLLECTION__", - "__FLATTEN__", "__APPLY_RULES__", + "__FLATTEN__", "tp_cat" ], "update_time": "2023-12-03", @@ -38842,18 +54054,18 @@ "generic" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -38882,14 +54094,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-30", "versions": 1 @@ -38918,14 +54130,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-30", "versions": 1 @@ -38939,20 +54151,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9f2d18f0d0896e8b", @@ -38968,22 +54180,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -38996,18 +54208,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "471eb8b4c54f897d", @@ -39023,19 +54235,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -39062,8 +54274,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-30", "versions": 1 @@ -39090,8 +54302,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-30", "versions": 1 @@ -39104,16 +54316,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "700fa3ab11a8f3e2", @@ -39129,16 +54341,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -39151,13 +54363,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -39173,19 +54385,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-30", "versions": 1 @@ -39198,19 +54410,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "bc87309a8763d0b4", @@ -39226,20 +54438,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -39253,10 +54465,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ae16643c04ad1216", @@ -39271,20 +54483,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-11-30", "versions": 1 @@ -39298,10 +54510,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8f9dc5ba61a02815", @@ -39316,19 +54528,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-30", "versions": 1 @@ -39342,10 +54554,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7582a48054c44d6e", @@ -39360,19 +54572,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-30", "versions": 1 @@ -39384,17 +54596,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d768c0e0df4d432e", @@ -39409,15 +54621,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -39429,14 +54641,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "614807d57979554c", @@ -39452,18 +54664,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -39486,15 +54698,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -39517,21 +54729,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -39554,21 +54766,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -39591,19 +54803,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -39631,8 +54843,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-30", "versions": 1 @@ -39660,17 +54872,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2023-11-30", "versions": 1 @@ -39696,20 +54908,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -39721,16 +54933,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "429ae28a178cd07c", @@ -39748,27 +54960,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -39780,15 +54992,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "a9e1a6b90dbd2518", @@ -39806,17 +55018,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -39839,11 +55051,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-11-24", "versions": 1 @@ -39853,9 +55065,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence analysis", + "Structural variation detection", "Pairwise sequence alignment", - "Structural variation detection" + "Sequence analysis" ], "edam_topic": [], "id": "35a9136ddf37d589", @@ -39872,10 +55084,10 @@ ], "tools": [ "samtools_calmd", + "samtools_stats", "samtools_sort", "minimap2", - "sniffles", - "samtools_stats" + "sniffles" ], "update_time": "2023-11-23", "versions": 15 @@ -39910,20 +55122,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1f2a1438e41188f2", @@ -39939,22 +55151,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-23", "versions": 1 @@ -39981,8 +55193,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-23", "versions": 1 @@ -39995,16 +55207,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d261bbd05889ce75", @@ -40020,16 +55232,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-23", "versions": 1 @@ -40042,13 +55254,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -40064,19 +55276,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-23", "versions": 1 @@ -40104,8 +55316,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-23", "versions": 1 @@ -40133,8 +55345,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-23", "versions": 1 @@ -40144,10 +55356,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence analysis", + "Structural variation detection", "Pairwise sequence alignment", - "Variant calling", - "Structural variation detection" + "Sequence analysis", + "Variant calling" ], "edam_topic": [], "id": "cb54883452a73019", @@ -40164,10 +55376,10 @@ ], "tools": [ "samtools_calmd", - "clair3", + "samtools_stats", "samtools_sort", + "clair3", "minimap2", - "samtools_stats", "sniffles" ], "update_time": "2023-11-21", @@ -40191,11 +55403,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-11-21", "versions": 2 @@ -40218,11 +55430,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-11-21", "versions": 2 @@ -40251,14 +55463,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-16", "versions": 1 @@ -40271,8 +55483,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "075c4126e66def01", @@ -40287,11 +55499,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-16", "versions": 1 @@ -40304,16 +55516,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0444c98a3ca2a3ca", @@ -40329,16 +55541,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-16", "versions": 1 @@ -40351,13 +55563,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -40373,19 +55585,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-16", "versions": 1 @@ -40399,10 +55611,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "71c4ec4805f83cd5", @@ -40417,20 +55629,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-11-16", "versions": 1 @@ -40444,10 +55656,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "db03a18167f26399", @@ -40462,19 +55674,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-16", "versions": 1 @@ -40488,10 +55700,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "45c5e0a1e10edc54", @@ -40506,19 +55718,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-16", "versions": 1 @@ -40532,20 +55744,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1e02a7292e9974b1", @@ -40561,22 +55773,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -40603,8 +55815,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -40631,8 +55843,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -40655,19 +55867,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2023-11-13", "versions": 1 @@ -40688,11 +55900,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2023-11-12", "versions": 0 @@ -40714,9 +55926,9 @@ "tags": [], "tools": [ "tp_cut_tool", - "obisindicators", "Filter1", - "csv_to_tabular" + "csv_to_tabular", + "obisindicators" ], "update_time": "2023-11-10", "versions": 2 @@ -40737,9 +55949,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "cb_dissim", "cb_ivr", - "cb_div", - "cb_dissim" + "cb_div" ], "update_time": "2023-11-10", "versions": 2 @@ -40762,11 +55974,11 @@ "tools": [ "cat1", "regex1", - "Remove beginning1", - "Grouping1", "tp_head_tool", + "tp_cat", "Grep1", - "tp_cat" + "Remove beginning1", + "Grouping1" ], "update_time": "2023-11-10", "versions": 5 @@ -40787,10 +55999,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ecoregion_clara_cluster", + "ecoregion_eco_map", "ecoregion_cluster_estimate", "ecoregion_taxa_seeker", - "ecoregion_eco_map", - "ecoregion_clara_cluster", "ecoregion_brt_analysis" ], "update_time": "2023-11-09", @@ -40812,10 +56024,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "srs_diversity_maps", + "srs_spectral_indices", "srs_preprocess_s2", "srs_global_indices", - "srs_spectral_indices" + "srs_diversity_maps" ], "update_time": "2023-11-09", "versions": 1 @@ -40836,11 +56048,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ecology_stat_presence_abs", "tool_anonymization", + "ecology_beta_diversity", "ecology_presence_abs_abund", "ecology_link_between_var", - "ecology_stat_presence_abs", - "ecology_beta_diversity", "ecology_homogeneity_normality" ], "update_time": "2023-11-09", @@ -40851,8 +56063,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequence analysis", "Sequencing quality control" ], @@ -40868,22 +56080,22 @@ "tags": [], "tools": [ "seq_filter_by_id", + "unzip", "obi_illumina_pairend", - "fastq_groomer", "obi_annotate", + "obi_stat", + "obi_tab", "wc_gnu", - "obi_ngsfilter", + "Filter1", + "ncbi_blastn_wrapper", + "obi_uniq", + "obi_clean", + "fastqc", "join1", "Cut1", - "unzip", - "obi_tab", - "obi_stat", - "fastqc", - "ncbi_blastn_wrapper", - "Filter1", "obi_grep", - "obi_clean", - "obi_uniq" + "obi_ngsfilter", + "fastq_groomer" ], "update_time": "2023-11-09", "versions": 0 @@ -40912,14 +56124,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-09", "versions": 1 @@ -40933,20 +56145,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f38745208494d4ab", @@ -40962,22 +56174,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -40991,20 +56203,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "270b6f82efab28b2", @@ -41020,22 +56232,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41049,20 +56261,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "002a51bdef00e14d", @@ -41078,22 +56290,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41106,18 +56318,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "a6dd62ab4b9a0725", @@ -41133,19 +56345,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41158,8 +56370,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "5bb7691b176d1010", @@ -41174,11 +56386,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-09", "versions": 1 @@ -41205,8 +56417,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -41233,8 +56445,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -41261,8 +56473,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -41275,16 +56487,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "bac84a7033c3423f", @@ -41300,16 +56512,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41322,16 +56534,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "915ffef5b14c871e", @@ -41347,16 +56559,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41369,16 +56581,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "ca39822372847670", @@ -41394,16 +56606,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41416,16 +56628,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9667bf36217083b7", @@ -41441,16 +56653,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -41463,13 +56675,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -41485,19 +56697,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-09", "versions": 1 @@ -41510,13 +56722,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -41532,19 +56744,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-09", "versions": 1 @@ -41554,10 +56766,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "cf196794bbd365d8", @@ -41570,11 +56782,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ip_2d_filter_segmentation_by_features", - "ip_2d_split_binaryimage_by_watershed", + "ip_2d_feature_extraction", "ip_filter_standard", + "ip_2d_filter_segmentation_by_features", "ip_threshold", - "ip_2d_feature_extraction" + "ip_2d_split_binaryimage_by_watershed" ], "update_time": "2023-11-07", "versions": 3 @@ -41608,8 +56820,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "cdf782de6c67477a", @@ -41622,8 +56834,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2023-11-02", "versions": 1 @@ -41636,8 +56848,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "72c03f7b5bc9fb9d", @@ -41663,15 +56875,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "14b9753269cd368f", @@ -41686,13 +56898,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-02", "versions": 1 @@ -41704,19 +56916,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "d83280cd72ec0f33", @@ -41731,27 +56943,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-02", "versions": 1 @@ -41763,19 +56975,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "111527fe542846af", @@ -41790,27 +57002,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-02", "versions": 1 @@ -41822,19 +57034,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "7e0ba4c14803448e", @@ -41849,27 +57061,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-02", "versions": 1 @@ -41881,15 +57093,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "79fd2517af48c594", @@ -41904,13 +57116,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-02", "versions": 1 @@ -41922,17 +57134,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5138874b208adb4b", @@ -41947,15 +57159,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-02", "versions": 1 @@ -41967,17 +57179,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "74e4a8f2edb25f1a", @@ -41992,15 +57204,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-02", "versions": 1 @@ -42021,10 +57233,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Cut1", "pepquery", - "Filter1", "Grouping1", - "Cut1" + "Filter1" ], "update_time": "2023-10-31", "versions": 6 @@ -42051,35 +57263,35 @@ "eosc4cancer" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "snpSift_extractFields", - "__FILTER_FROM_FILE__", - "export_remote", - "split_file_to_collection", - "__BUILD_LIST__", - "vcfanno", - "ensembl_vep", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", - "snpSift_filter", - "Add_a_column1", - "datamash_transpose", + "snpSift_extractFields", "collapse_dataset", + "tp_find_and_replace", + "tp_tail_tool", + "bg_column_arrange_by_header", "add_line_to_file", + "ensembl_vep", "param_value_from_file", - "compose_text_param", + "Filter1", + "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "__BUILD_LIST__", "__SORTLIST__", - "__RELABEL_FROM_FILE__", + "bcftools_plugin_split_vep", + "tp_easyjoin_tool", + "export_remote", + "compose_text_param", "tp_replace_in_column", - "tp_tail_tool", + "__RELABEL_FROM_FILE__", + "datamash_ops", + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "snpSift_filter", "Cut1", - "bcftools_plugin_split_vep", - "vcf2maf", - "Filter1" + "__FILTER_FROM_FILE__" ], "update_time": "2023-10-27", "versions": 15 @@ -42091,15 +57303,15 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Variant calling", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "af30010868c97316", @@ -42114,28 +57326,28 @@ "eosc4cancer" ], "tools": [ - "samtools_view", + "__EXTRACT_DATASET__", + "trimmomatic", + "collapse_dataset", + "Grep1", "fastqc", - "split_file_to_collection", + "__APPLY_RULES__", + "qualimap_bamqc", + "samtools_calmd", + "multiqc", "__BUILD_LIST__", - "__EXTRACT_DATASET__", - "tp_replace_in_line", + "Convert characters1", + "bwa_mem", "pick_value", - "tp_text_file_with_recurring_lines", "bamleftalign", - "collapse_dataset", + "samtools_view", "compose_text_param", - "Convert characters1", - "__APPLY_RULES__", + "tp_replace_in_line", "__RELABEL_FROM_FILE__", - "qualimap_bamqc", "varscan_somatic", - "bwa_mem", - "samtools_calmd", - "trimmomatic", "samtools_rmdup", - "multiqc", - "Grep1" + "split_file_to_collection", + "tp_text_file_with_recurring_lines" ], "update_time": "2023-10-27", "versions": 13 @@ -42162,15 +57374,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-10-26", "versions": 1 @@ -42183,19 +57395,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "92760fc19ef120ce", @@ -42211,20 +57423,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2023-10-26", "versions": 1 @@ -42245,17 +57457,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2023-10-25", "versions": 6 @@ -42278,11 +57490,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_ops", "regexColumn1", "scanpy_read_10x", - "tp_grep_tool", - "retrieve_scxa" + "retrieve_scxa", + "anndata_ops", + "tp_grep_tool" ], "update_time": "2023-10-21", "versions": 3 @@ -42294,17 +57506,17 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Differential gene expression analysis", - "Read summarisation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "bc79a9f797334b01", @@ -42319,13 +57531,13 @@ "mirna" ], "tools": [ - "volcanoplot", - "trim_galore", + "bowtie2", "featurecounts", - "__TAG_FROM_FILE__", + "trim_galore", + "volcanoplot", "fastqc", - "deseq2", - "bowtie2" + "__TAG_FROM_FILE__", + "deseq2" ], "update_time": "2023-10-20", "versions": 8 @@ -42349,8 +57561,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2023-10-19", @@ -42361,14 +57573,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "d789165f4e0c50eb", @@ -42381,8 +57593,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "Grep1", + "Cut1", "Grouping1", "maxquant" ], @@ -42407,14 +57619,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2023-10-19", "versions": 1 @@ -42443,24 +57655,24 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "anndata_ops", - "anndata_manipulate", - "join1", "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "anndata_ops", + "anndata_manipulate", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2023-10-13", "versions": 4 @@ -42487,31 +57699,31 @@ "eosc4cancer" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "snpSift_extractFields", - "__FILTER_FROM_FILE__", - "split_file_to_collection", - "__BUILD_LIST__", - "vcfanno", - "ensembl_vep", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", - "snpSift_filter", - "Add_a_column1", - "datamash_transpose", + "snpSift_extractFields", "collapse_dataset", + "tp_find_and_replace", + "Cut1", + "bg_column_arrange_by_header", "add_line_to_file", + "ensembl_vep", + "Filter1", + "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "__BUILD_LIST__", "__SORTLIST__", - "__RELABEL_FROM_FILE__", - "tp_replace_in_column", - "Cut1", "bcftools_plugin_split_vep", - "vcf2maf", - "Filter1" + "tp_easyjoin_tool", + "tp_replace_in_column", + "__RELABEL_FROM_FILE__", + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "snpSift_filter", + "datamash_ops", + "__FILTER_FROM_FILE__" ], "update_time": "2023-10-10", "versions": 10 @@ -42534,8 +57746,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bigwig_average", - "__APPLY_RULES__" + "__APPLY_RULES__", + "deeptools_bigwig_average" ], "update_time": "2023-10-05", "versions": 1 @@ -42547,19 +57759,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "d12617d0df5f81d0", @@ -42574,27 +57786,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-10-05", "versions": 1 @@ -42622,8 +57834,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-10-05", "versions": 1 @@ -42633,16 +57845,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "607ca3a9d45bd080", @@ -42656,22 +57868,22 @@ "tags": [], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2023-10-03", "versions": 5 @@ -42681,10 +57893,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -42722,8 +57934,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bigwig_average", - "__APPLY_RULES__" + "__APPLY_RULES__", + "deeptools_bigwig_average" ], "update_time": "2023-09-28", "versions": 1 @@ -42749,8 +57961,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "repeatmasker_wrapper", - "repeatmodeler" + "repeatmodeler", + "repeatmasker_wrapper" ], "update_time": "2023-09-28", "versions": 1 @@ -42762,19 +57974,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "8132c3b710fd6d48", @@ -42789,27 +58001,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-09-28", "versions": 1 @@ -42834,9 +58046,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-21", @@ -42849,15 +58061,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "6ebd09100fc98878", @@ -42872,18 +58084,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -42895,14 +58107,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "406e6ef0dfb38628", @@ -42917,14 +58129,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -42936,15 +58148,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "d3edc3f0659a5e5b", @@ -42959,17 +58171,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -42981,14 +58193,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "bace9aebab9d4ce3", @@ -43003,14 +58215,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -43031,15 +58243,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Extract genomic DNA 1", - "Add_a_column1", - "join1", - "Cut1", + "Paste1", "sort1", + "Add_a_column1", + "gops_join_1", + "Extract genomic DNA 1", "CONVERTER_uncompressed_to_gz", "Grouping1", - "gops_join_1", - "Paste1" + "join1", + "Cut1" ], "update_time": "2023-09-20", "versions": 4 @@ -43060,15 +58272,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sort1", "Add_a_column1", - "tp_cut_tool", - "join1", + "tp_head_tool", + "build_ucsc_custom_track_1", + "gops_join_1", "comp1", - "sort1", "Grouping1", - "build_ucsc_custom_track_1", - "tp_head_tool", - "gops_join_1" + "join1", + "tp_cut_tool" ], "update_time": "2023-09-19", "versions": 3 @@ -43093,14 +58305,14 @@ "name:single-cell" ], "tools": [ - "scanpy_run_fdg", - "anndata_manipulate", - "scanpy_run_paga", "scanpy_plot_trajectory", - "scanpy_compute_graph", "scanpy_run_diffmap", + "scanpy_run_paga", + "anndata_manipulate", + "scanpy_run_fdg", + "scanpy_run_dpt", "scanpy_plot_embed", - "scanpy_run_dpt" + "scanpy_compute_graph" ], "update_time": "2023-09-19", "versions": 7 @@ -43138,14 +58350,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", - "Genome alignment", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Generation" + "Genome alignment", + "Read mapping", + "Filtering" ], "edam_topic": [], "id": "3fb550d7c2bc390a", @@ -43158,12 +58370,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ivar_consensus", + "fastp", "bwa_mem", - "read_it_and_keep", - "samtools_view", "fasta_regex_finder", - "fastp", - "ivar_consensus", + "samtools_view", + "read_it_and_keep", "qualimap_bamqc" ], "update_time": "2023-09-13", @@ -43174,10 +58386,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -43191,10 +58403,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metanovo", - "fasta_merge_files_and_filter_unique_sequences", "uniprotxml_downloader", - "dbbuilder" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder", + "metanovo" ], "update_time": "2023-09-07", "versions": 7 @@ -43208,10 +58420,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5385abe9c2589b69", @@ -43226,20 +58438,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-09-07", "versions": 1 @@ -43253,10 +58465,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "16080c3c1488a8b5", @@ -43271,19 +58483,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-09-07", "versions": 1 @@ -43297,10 +58509,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0fb12e3a127fc4be", @@ -43315,19 +58527,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-09-07", "versions": 1 @@ -43352,9 +58564,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-09-07", "versions": 1 @@ -43379,9 +58591,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-07", @@ -43407,9 +58619,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-09-07", "versions": 1 @@ -43438,8 +58650,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-09-07", @@ -43494,9 +58706,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-07", @@ -43526,8 +58738,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-09-07", @@ -43569,19 +58781,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "54b91dd86f463391", @@ -43596,26 +58808,26 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -43627,17 +58839,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "146cef3acb2eba75", @@ -43652,15 +58864,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-09-07", "versions": 1 @@ -43688,8 +58900,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-09-07", "versions": 1 @@ -43718,21 +58930,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly", - "Read alignment", - "Read mapping", - "Sequencing quality control", - "Genome assembly", - "Sequence assembly validation", + "Gene prediction", + "Genome annotation", + "Sequence contamination filtering", "Visualisation", + "Genome assembly", "Analysis", - "Sequence contamination filtering", + "Sequence assembly", + "Sequencing quality control", "Scaffolding", - "Taxonomic classification", - "Gene prediction", + "Transcriptome assembly", "Coding region prediction", - "Genome annotation", - "Transcriptome assembly" + "Read alignment", + "Sequence assembly validation", + "Read mapping", + "Taxonomic classification" ], "edam_topic": [], "id": "007ce6405d196df3", @@ -43745,16 +58957,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "kraken2", - "staramr_search", - "quast", - "taxonomy_krona_chart", - "fastp", + "bowtie2", "pilon", - "busco", "prokka", + "kraken2", "spades", - "bowtie2" + "fastp", + "taxonomy_krona_chart", + "quast", + "busco", + "staramr_search" ], "update_time": "2023-09-03", "versions": 6 @@ -43777,13 +58989,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2023-09-01", "versions": 3 @@ -43808,9 +59020,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-08-31", @@ -43823,15 +59035,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fa0ff9a0db8bbddb", @@ -43846,13 +59058,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-08-31", "versions": 1 @@ -43864,15 +59076,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fd6429a788660c8d", @@ -43887,13 +59099,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-08-31", "versions": 1 @@ -43903,9 +59115,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Read binning", - "Sequence clustering" + "Sequence clustering", + "Read mapping" ], "edam_topic": [], "id": "58f779d238d569dc", @@ -43918,14 +59130,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "concoct_extract_fasta_bins", + "samtools_sort", + "concoct_merge_cut_up_clustering", + "concoct", "concoct_coverage_table", - "concoct_cut_up_fasta", "samtools_view", - "concoct", - "concoct_merge_cut_up_clustering", - "samtools_sort", - "bowtie2" + "concoct_cut_up_fasta" ], "update_time": "2023-08-28", "versions": 2 @@ -43967,9 +59179,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", + "interactive_tool_ml_jupyter_notebook", "Filter1", - "interactive_tool_ml_jupyter_notebook" + "Cut1" ], "update_time": "2023-08-17", "versions": 3 @@ -44020,13 +59232,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Visualisation", "Sequence contamination filtering", + "Visualisation", "Statistical calculation", + "Genome assembly", + "Sequencing quality control", + "Aggregation", + "Sequence composition calculation", "Taxonomic classification" ], "edam_topic": [], @@ -44041,11 +59253,11 @@ "tags": [], "tools": [ "kraken2", - "taxonomy_krona_chart", + "krakentools_kreport2krona", "fastp", "megahit", - "fastqc", - "krakentools_kreport2krona" + "taxonomy_krona_chart", + "fastqc" ], "update_time": "2023-07-29", "versions": 0 @@ -44079,12 +59291,12 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", + "Genome indexing", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "63eed9c2e025a723", @@ -44097,13 +59309,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", + "collapse_dataset", "fastp", - "lofreq_call", - "multiqc" + "multiqc", + "tp_sort_header_tool", + "bwa_mem", + "lofreq_call" ], "update_time": "2023-07-25", "versions": 2 @@ -44113,8 +59325,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Visualisation", "Classification", + "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -44139,8 +59351,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Visualisation", "Classification", + "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -44165,16 +59377,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "c4119ea7ffd29094", @@ -44188,22 +59400,22 @@ "tags": [], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2023-07-19", "versions": 9 @@ -44215,15 +59427,15 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", - "Local alignment", - "Variant calling", - "Sequence alignment", "Phylogenetic tree generation", + "Sequence alignment", + "Local alignment", + "Sequence alignment analysis", + "Sequence analysis", "Global alignment", "Phylogenetic tree visualisation", - "Sequence analysis" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "b681f7b677b23168", @@ -44236,16 +59448,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", - "filter_by_fasta_ids", + "bowtie2", "EMBOSS: transeq101", - "snippy_clean_full_aln", - "tp_sed_tool", - "fastq_trimmer", + "fastq_to_fasta_python", "bioext_bam2msa", "cshl_fasta_formatter", - "bowtie2", - "fastq_to_fasta_python" + "tp_sed_tool", + "filter_by_fasta_ids", + "snippy_clean_full_aln", + "fastq_trimmer", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2023-07-14", "versions": 26 @@ -44266,21 +59478,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2023-07-14", "versions": 6 @@ -44301,21 +59513,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2023-07-14", "versions": 8 @@ -44336,21 +59548,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2023-07-14", "versions": 17 @@ -44371,21 +59583,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_makendx", + "gromacs_modify_topology", + "gmx_solvate", + "gmx_rmsf", "__EXTRACT_DATASET__", - "gmx_editconf", - "tleap", + "gmx_trj", + "gmx_rmsd", "gmx_get_builtin_file", - "gmx_solvate", - "tp_grep_tool", + "tleap", + "gmx_makendx", "acpype_Amber2Gromacs", - "gmx_sim", - "gmx_rmsd", "gmx_restraints", - "gmx_trj", - "gmx_rmsf", - "gromacs_modify_topology", - "gmx_em" + "gmx_editconf", + "gmx_em", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2023-07-14", "versions": 10 @@ -44408,12 +59620,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scanpy_compute_graph", - "scanpy_parameter_iterator", - "scanpy_plot_embed", "scanpy_run_tsne", "scanpy_find_cluster", - "scanpy_run_umap" + "scanpy_parameter_iterator", + "scanpy_plot_embed", + "scanpy_run_umap", + "scanpy_compute_graph" ], "update_time": "2023-07-14", "versions": 14 @@ -44434,19 +59646,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_model_fit", + "sklearn_clf_metrics", + "sklearn_searchcv", + "param_value_from_file", "datamash_transpose", - "table_compute", - "keras_model_config", - "tp_sort_header_tool", "wc_gnu", - "param_value_from_file", - "sklearn_train_test_split", "model_prediction", "compose_text_param", - "sklearn_searchcv", - "sklearn_clf_metrics", - "keras_model_builder" + "sklearn_model_fit", + "table_compute", + "tp_sort_header_tool", + "keras_model_config", + "keras_model_builder", + "sklearn_train_test_split" ], "update_time": "2023-07-13", "versions": 7 @@ -44469,10 +59681,10 @@ "tools": [ "cat1", "sklearn_data_preprocess", + "tp_head_tool", "table_compute", - "sklearn_feature_selection", "csv_to_tabular", - "tp_head_tool" + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 4 @@ -44495,10 +59707,10 @@ "tools": [ "cat1", "sklearn_data_preprocess", + "tp_head_tool", "table_compute", - "sklearn_feature_selection", "csv_to_tabular", - "tp_head_tool" + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 7 @@ -44519,19 +59731,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sklearn_clf_metrics", "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "sklearn_clf_metrics" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 9 @@ -44552,19 +59764,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sklearn_clf_metrics", "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", "comp1", - "sklearn_train_test_split", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "sklearn_clf_metrics" + "sklearn_train_test_split", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 2 @@ -44585,19 +59797,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sklearn_clf_metrics", "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", "comp1", - "sklearn_train_test_split", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "sklearn_clf_metrics" + "sklearn_train_test_split", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 24 @@ -44619,22 +59831,22 @@ "tags": [], "tools": [ "cat1", - "sklearn_model_fit", + "param_value_from_file", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", - "table_compute", - "keras_model_config", - "tp_sort_header_tool", "wc_gnu", - "param_value_from_file", - "comp1", + "tp_head_tool", "model_prediction", - "sklearn_feature_selection", "compose_text_param", + "sklearn_model_fit", + "table_compute", + "tp_sort_header_tool", + "comp1", + "keras_model_config", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "keras_model_builder" + "keras_model_builder", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 6 @@ -44656,22 +59868,22 @@ "tags": [], "tools": [ "cat1", - "sklearn_model_fit", + "param_value_from_file", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", - "table_compute", - "keras_model_config", - "tp_sort_header_tool", "wc_gnu", - "param_value_from_file", - "comp1", + "tp_head_tool", "model_prediction", - "sklearn_feature_selection", "compose_text_param", + "sklearn_model_fit", + "table_compute", + "tp_sort_header_tool", + "comp1", + "keras_model_config", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "keras_model_builder" + "keras_model_builder", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 49 @@ -44693,17 +59905,17 @@ "tags": [], "tools": [ "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 7 @@ -44725,17 +59937,17 @@ "tags": [], "tools": [ "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 2 @@ -44757,16 +59969,16 @@ "tags": [], "tools": [ "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", - "table_compute", + "sklearn_build_pipeline", "sklearn_model_validation", - "comp1", + "tp_head_tool", "model_prediction", - "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool" + "table_compute", + "comp1", + "csv_to_tabular" ], "update_time": "2023-07-13", "versions": 16 @@ -44788,17 +60000,17 @@ "tags": [], "tools": [ "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 27 @@ -44819,19 +60031,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sklearn_clf_metrics", "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool", - "sklearn_clf_metrics" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-13", "versions": 11 @@ -44852,8 +60064,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", "uniprotxml_downloader", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder" ], "update_time": "2023-07-13", @@ -44864,9 +60076,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "71cac07a151f9470", @@ -44879,8 +60091,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-07-13", "versions": 0 @@ -44890,10 +60102,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -44932,9 +60144,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_sed_tool", "filter_by_fasta_ids", - "cshl_fasta_formatter", - "tp_sed_tool" + "cshl_fasta_formatter" ], "update_time": "2023-07-12", "versions": 3 @@ -44946,10 +60158,10 @@ "edam_operation": [ "Pairwise sequence alignment", "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "90f993a1b245eb68", @@ -44962,15 +60174,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", - "trimmomatic", "EMBOSS: transeq101", + "minimap2", + "fastq_to_fasta_python", + "trimmomatic", "bioext_bealign", - "tp_sed_tool", "bioext_bam2msa", - "minimap2", "cshl_fasta_formatter", - "fastq_to_fasta_python" + "tp_sed_tool", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2023-07-11", "versions": 16 @@ -44998,18 +60210,18 @@ "variant-analysis" ], "tools": [ - "bcftools_norm", "regexColumn1", + "Filter1", "bcftools_merge", - "gemini_load", - "tp_grep_tool", "snpEff", - "gene_iobio_display_generation_iframe", - "CONVERTER_uncompressed_to_gz", + "gemini_load", + "bcftools_norm", "gemini_inheritance", + "CONVERTER_uncompressed_to_gz", + "CONVERTER_gz_to_uncompressed", + "tp_grep_tool", "pyega3", - "Filter1", - "CONVERTER_gz_to_uncompressed" + "gene_iobio_display_generation_iframe" ], "update_time": "2023-07-11", "versions": 76 @@ -45059,17 +60271,17 @@ "tags": [], "tools": [ "cat1", - "sklearn_build_pipeline", + "sklearn_searchcv", "sklearn_data_preprocess", "datamash_transpose", + "sklearn_build_pipeline", + "tp_head_tool", + "model_prediction", "table_compute", - "tp_cut_tool", "comp1", - "model_prediction", - "sklearn_feature_selection", "csv_to_tabular", - "sklearn_searchcv", - "tp_head_tool" + "tp_cut_tool", + "sklearn_feature_selection" ], "update_time": "2023-07-10", "versions": 62 @@ -45079,8 +60291,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -45094,9 +60306,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "freebayes", - "bowtie2", "snpSift_filter", + "bowtie2", + "freebayes", "trimmomatic" ], "update_time": "2023-07-08", @@ -45118,8 +60330,8 @@ "doi": "", "edam_operation": [ "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" + "Phylogenetic analysis", + "Taxonomic classification" ], "edam_topic": [], "id": "a7a6d8ecc2795f58", @@ -45137,16 +60349,16 @@ "name:functionalprofiling" ], "tools": [ - "combine_metaphlan2_humann2", - "Cut1", - "tp_find_and_replace", - "humann_renorm_table", - "humann", "humann_regroup_table", + "humann_rename_table", + "humann", + "tp_find_and_replace", + "combine_metaphlan2_humann2", + "Grep1", "humann_unpack_pathways", "humann_split_stratified_table", - "Grep1", - "humann_rename_table" + "Cut1", + "humann_renorm_table" ], "update_time": "2023-07-07", "versions": 3 @@ -45159,14 +60371,14 @@ ], "doi": "", "edam_operation": [ - "Conversion", - "Phylogenetic tree analysis", "Visualisation", + "Nucleic acid sequence analysis", + "Phylogenetic tree editing", + "Phylogenetic tree analysis", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Nucleic acid sequence analysis", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "05f5f040337786bf", @@ -45184,12 +60396,12 @@ "name:communityprofiling" ], "tools": [ - "metaphlan", + "export2graphlan", "graphlan_annotate", - "Cut1", - "graphlan", "taxonomy_krona_chart", - "export2graphlan" + "graphlan", + "metaphlan", + "Cut1" ], "update_time": "2023-07-06", "versions": 3 @@ -45209,14 +60421,14 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence comparison", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence comparison", + "Sequence similarity search", + "Sequence composition calculation", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", "Validation" ], @@ -45237,10 +60449,10 @@ ], "tools": [ "bg_sortmerna", - "fastq_paired_end_interlacer", "multiqc", - "fastqc", + "fastq_paired_end_interlacer", "__FLATTEN__", + "fastqc", "cutadapt" ], "update_time": "2023-07-06", @@ -45251,8 +60463,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", + "Sequencing quality control", "Taxonomic classification" ], "edam_topic": [], @@ -45266,11 +60478,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seq_filter_by_id", + "filter_tabular", "kraken2", - "porechop", "fastp", - "filter_tabular" + "porechop", + "seq_filter_by_id" ], "update_time": "2023-07-04", "versions": 1 @@ -45295,14 +60507,14 @@ "tools": [ "seq_filter_by_id", "obi_illumina_pairend", - "obi_uniq", "obi_annotate", - "join1", - "obi_tab", "ncbi_blastn_wrapper", - "obi_grep", + "obi_uniq", + "join1", "obi_clean", - "obi_stat" + "obi_grep", + "obi_stat", + "obi_tab" ], "update_time": "2023-06-30", "versions": 0 @@ -45323,8 +60535,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", "uniprotxml_downloader", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder" ], "update_time": "2023-06-20", @@ -45353,31 +60565,31 @@ "cancer" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "snpSift_extractFields", - "__FILTER_FROM_FILE__", - "split_file_to_collection", - "__BUILD_LIST__", - "vcfanno", - "ensembl_vep", "__EXTRACT_DATASET__", - "tp_find_and_replace", - "__MERGE_COLLECTION__", - "datamash_ops", - "tp_text_file_with_recurring_lines", - "snpSift_filter", - "Add_a_column1", - "datamash_transpose", + "snpSift_extractFields", "collapse_dataset", + "tp_find_and_replace", + "Cut1", + "bg_column_arrange_by_header", "add_line_to_file", + "ensembl_vep", + "Filter1", + "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "__BUILD_LIST__", "__SORTLIST__", - "__RELABEL_FROM_FILE__", - "tp_replace_in_column", - "Cut1", "bcftools_plugin_split_vep", - "vcf2maf", - "Filter1" + "tp_easyjoin_tool", + "tp_replace_in_column", + "__RELABEL_FROM_FILE__", + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "snpSift_filter", + "datamash_ops", + "__FILTER_FROM_FILE__" ], "update_time": "2023-06-19", "versions": 9 @@ -45389,18 +60601,18 @@ ], "doi": "", "edam_operation": [ - "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", "Copy number estimation", + "Sequence alignment", + "Genome alignment", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "2c3d05023c02113e", @@ -45415,33 +60627,33 @@ "cancer" ], "tools": [ - "samtools_view", - "fastqc", - "circos", - "__BUILD_LIST__", - "split_file_to_collection", "__EXTRACT_DATASET__", - "tp_replace_in_line", - "tp_text_file_with_recurring_lines", - "Add_a_column1", - "bamleftalign", + "trimmomatic", "collapse_dataset", + "Grep1", + "fastqc", + "__APPLY_RULES__", "add_line_to_file", + "qualimap_bamqc", + "samtools_calmd", "param_value_from_file", - "compose_text_param", + "Add_a_column1", + "multiqc", + "__BUILD_LIST__", "Convert characters1", - "__APPLY_RULES__", + "bwa_mem", + "bamleftalign", + "samtools_view", + "compose_text_param", + "tp_replace_in_line", "__RELABEL_FROM_FILE__", - "qualimap_bamqc", "varscan_somatic", - "bwa_mem", - "samtools_calmd", - "trimmomatic", - "Cut1", "samtools_rmdup", - "multiqc", "control_freec", - "Grep1" + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "circos", + "Cut1" ], "update_time": "2023-06-19", "versions": 11 @@ -45476,21 +60688,21 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Sequence annotation", + "Sequence comparison", + "Transcriptome assembly", "Sequence composition calculation", "De-novo assembly", - "Sequence annotation", - "Sequencing quality control", "Protein sequence analysis", - "Sequence alignment", - "Sequence comparison", - "Sequence assembly validation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq analysis", "Sequence analysis", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9b025479fade745d", @@ -45507,36 +60719,36 @@ "name:transcriptomics" ], "tools": [ - "isoformswitchanalyzer", - "rseqc_read_distribution", - "__FILTER_FROM_FILE__", + "rseqc_junction_annotation", + "rseqc_geneBody_coverage", + "tp_cat", + "fastqc", + "rna_star", + "gene2exon1", "tp_grep_tool", "rseqc_infer_experiment", - "fastp", - "fastqc", - "rna_quast", - "rseqc_junction_saturation", - "pfamscan", - "gffread", - "stringtie_merge", + "param_value_from_file", "sort1", + "multiqc", "tp_sort_header_tool", - "rseqc_inner_distance", - "param_value_from_file", - "gtftobed12", "__FLATTEN__", - "stringtie", - "rseqc_junction_annotation", "cpat", - "gene2exon1", - "tp_awk_tool", - "Cut1", - "rna_star", + "stringtie", + "gffread", + "rseqc_junction_saturation", "tp_sorted_uniq", + "rseqc_inner_distance", + "rseqc_read_distribution", + "isoformswitchanalyzer", + "stringtie_merge", + "fastp", + "rna_quast", + "gtftobed12", "Remove beginning1", - "rseqc_geneBody_coverage", - "multiqc", - "tp_cat" + "Cut1", + "__FILTER_FROM_FILE__", + "tp_awk_tool", + "pfamscan" ], "update_time": "2023-06-11", "versions": 103 @@ -45546,22 +60758,22 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", + "Genome annotation", + "Visualisation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly", + "Mapping assembly", + "Scaffolding", "Base-calling", + "Cross-assembly", + "Box-Whisker plot plotting", "Transcriptome assembly", + "Coding region prediction", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Box-Whisker plot plotting", - "Sequence assembly validation", - "Visualisation", - "Scaffolding", - "Gene prediction", - "Genome annotation", - "Genome assembly", - "Coding region prediction", - "Mapping assembly", - "Cross-assembly" + "Sequence assembly validation" ], "edam_topic": [], "id": "cf8591391a17a914", @@ -45577,12 +60789,12 @@ "wgs" ], "tools": [ + "prokka", "flye", "nanoplot", "quast", - "medaka_consensus_pipeline", "busco", - "prokka" + "medaka_consensus_pipeline" ], "update_time": "2023-06-08", "versions": 10 @@ -45592,19 +60804,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Variant calling", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", - "Read pre-processing", + "Sequencing quality control", "Sequence trimming", + "Read summarisation", + "Formatting", + "Sequence composition calculation", + "Read pre-processing", + "Variant calling", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "cc37667c2d1f9056", @@ -45617,22 +60829,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "picard_MarkDuplicates", - "rna_star", - "rseqc_read_distribution", - "samtools_view", - "fastq_dump", - "rseqc_infer_experiment", - "featurecounts", - "gtftobed12", - "freebayes", - "hisat2", "rseqc_geneBody_coverage", + "freebayes", + "featurecounts", + "samtools_idxstats", "multiqc", + "gtftobed12", + "rseqc_infer_experiment", "__FLATTEN__", - "samtools_idxstats", - "cutadapt" + "fastqc", + "rna_star", + "hisat2", + "cutadapt", + "fastq_dump", + "samtools_view", + "rseqc_read_distribution", + "picard_MarkDuplicates" ], "update_time": "2023-06-06", "versions": 0 @@ -45662,12 +60874,12 @@ "nanopore" ], "tools": [ - "bcftools_norm", - "snpSift_extractFields", "bcftools_consensus", + "snpSift_extractFields", + "bcftools_norm", "clair3", - "minimap2", - "snpSift_filter" + "snpSift_filter", + "minimap2" ], "update_time": "2023-05-30", "versions": 8 @@ -45680,16 +60892,16 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", + "Multilocus sequence typing", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Multilocus sequence typing", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "2b888e200dfd91bc", @@ -45706,18 +60918,18 @@ ], "tools": [ "cat1", - "abricate", - "fasta2tab", "flye", - "mlst", - "Cut1", - "bandage_image", - "tp_find_and_replace", "add_line_to_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", - "tp_replace_in_column" + "abricate", + "fasta2tab", + "bandage_image", + "tp_replace_in_column", + "medaka_consensus_pipeline", + "Cut1", + "mlst" ], "update_time": "2023-05-30", "versions": 20 @@ -45746,9 +60958,9 @@ "nanopore" ], "tools": [ + "interactive_tool_phinch", "kraken_biom", - "kraken2", - "interactive_tool_phinch" + "kraken2" ], "update_time": "2023-05-30", "versions": 4 @@ -45761,9 +60973,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "ed2df13cfbc86b99", @@ -45794,14 +61006,14 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Sequence composition calculation", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "889f2782ad82bd69", @@ -45817,14 +61029,14 @@ "nanopore" ], "tools": [ - "seq_filter_by_id", - "kraken2", - "porechop", - "nanoplot", "filter_tabular", + "kraken2", "fastp", "multiqc", - "fastqc" + "nanoplot", + "porechop", + "fastqc", + "seq_filter_by_id" ], "update_time": "2023-05-30", "versions": 6 @@ -45845,12 +61057,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "stacks2_cstacks", - "stacks2_gstacks", - "stacks2_populations", "stacks2_tsv2bam", + "stacks2_ustacks", + "stacks2_populations", + "stacks2_cstacks", "stacks2_sstacks", - "stacks2_ustacks" + "stacks2_gstacks" ], "update_time": "2023-05-25", "versions": 2 @@ -45860,9 +61072,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", + "Sequence contamination filtering", "Sequencing quality control", - "Sequence contamination filtering" + "Read mapping" ], "edam_topic": [], "id": "25850714d13f0b0f", @@ -45878,14 +61090,14 @@ "resistome" ], "tools": [ - "resistome_analyzer", + "bowtie2", "rarefaction_analyzer", "samtools_sort", - "XY_Plot_1", + "resistome_analyzer", "fastp", - "bowtie2", + "bam_to_sam", "snpfinder", - "bam_to_sam" + "XY_Plot_1" ], "update_time": "2023-05-23", "versions": 0 @@ -45906,11 +61118,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", "tabular_to_csv", - "csv_to_tabular", - "Filter1" + "csv_to_tabular" ], "update_time": "2023-05-20", "versions": 0 @@ -45922,18 +61134,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Protein sequence analysis", - "Sequence alignment", - "Sequence comparison", "Sequence contamination filtering", "Statistical calculation", - "RNA-Seq analysis", + "Sequence alignment", + "Sequencing quality control", + "Sequence comparison", + "Transcriptome assembly", + "Sequence composition calculation", + "Protein sequence analysis", "Sequence analysis", "Validation", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1f9a9a7998ef5ab3", @@ -45950,27 +61162,27 @@ "name:transcriptomics" ], "tools": [ - "isoformswitchanalyzer", - "rseqc_read_distribution", - "__FILTER_FROM_FILE__", - "rseqc_infer_experiment", - "tp_grep_tool", - "fastp", - "fastqc", - "rseqc_junction_saturation", - "pfamscan", - "gtftobed12", - "stringtie", - "__FLATTEN__", "rseqc_junction_annotation", - "cpat", + "rseqc_geneBody_coverage", + "tp_cat", + "fastqc", "rna_star", + "tp_grep_tool", + "rseqc_infer_experiment", "collection_element_identifiers", - "tp_awk_tool", - "Remove beginning1", - "rseqc_geneBody_coverage", "multiqc", - "tp_cat" + "__FLATTEN__", + "cpat", + "stringtie", + "rseqc_junction_saturation", + "rseqc_read_distribution", + "isoformswitchanalyzer", + "fastp", + "gtftobed12", + "Remove beginning1", + "__FILTER_FROM_FILE__", + "tp_awk_tool", + "pfamscan" ], "update_time": "2023-05-20", "versions": 0 @@ -46001,12 +61213,12 @@ "face1174" ], "tools": [ - "Extract genomic DNA 1", - "ivar_variants", - "picard_FastqToSam", "CONVERTER_interval_to_bed_0", + "ivar_variants", + "Extract genomic DNA 1", + "blockbuster", "CONVERTER_gz_to_uncompressed", - "blockbuster" + "picard_FastqToSam" ], "update_time": "2023-05-20", "versions": 2 @@ -46027,9 +61239,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_sort_header_tool", "datamash_ops", - "tabular_to_csv", - "tp_sort_header_tool" + "tabular_to_csv" ], "update_time": "2023-05-19", "versions": 1 @@ -46052,10 +61264,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 2 @@ -46078,10 +61290,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46104,10 +61316,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46152,10 +61364,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46176,8 +61388,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tabular_to_csv", - "tp_sort_header_tool" + "tp_sort_header_tool", + "tabular_to_csv" ], "update_time": "2023-05-19", "versions": 1 @@ -46200,10 +61412,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46226,10 +61438,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46252,10 +61464,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46278,10 +61490,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46304,10 +61516,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2023-05-19", "versions": 1 @@ -46317,14 +61529,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "52cafb62f5bf6e25", @@ -46338,10 +61550,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 1 @@ -46351,14 +61563,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "61e592bafd9d2b58", @@ -46372,10 +61584,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 3 @@ -46385,14 +61597,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "50758631a0e81a7a", @@ -46406,10 +61618,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 2 @@ -46419,14 +61631,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "7c9b182da21748c7", @@ -46440,10 +61652,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 1 @@ -46453,14 +61665,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "60e4d0db3164f037", @@ -46474,10 +61686,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 2 @@ -46487,14 +61699,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "1bc7b5eabea972fd", @@ -46508,10 +61720,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 2 @@ -46521,14 +61733,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "bfb762c96328e3c1", @@ -46542,10 +61754,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 2 @@ -46555,14 +61767,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "212c213f1d8e0154", @@ -46576,10 +61788,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 1 @@ -46589,14 +61801,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "daf47855afa73de8", @@ -46610,10 +61822,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 1 @@ -46623,14 +61835,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "2d64d6571e01809d", @@ -46644,10 +61856,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 1 @@ -46657,14 +61869,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "ecab5b2c3ff3df9d", @@ -46678,10 +61890,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-19", "versions": 3 @@ -46691,14 +61903,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "910570a2caafe462", @@ -46712,10 +61924,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46725,14 +61937,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "a6c666f3028ea440", @@ -46746,10 +61958,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 3 @@ -46759,14 +61971,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "d5333903ba947adf", @@ -46780,10 +61992,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46793,14 +62005,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "766ebba7a2aee494", @@ -46814,10 +62026,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46827,14 +62039,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "a72d2667a53830f7", @@ -46848,10 +62060,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46861,14 +62073,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "88b382a6f56a6329", @@ -46882,10 +62094,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46895,14 +62107,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "bcb8a8c5bff790ab", @@ -46916,10 +62128,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46929,14 +62141,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "56868483be18f1a1", @@ -46950,10 +62162,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 1 @@ -46963,14 +62175,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "39876e9c04aad543", @@ -46984,10 +62196,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 0 @@ -46997,14 +62209,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "625aafb9cf16b03f", @@ -47018,10 +62230,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 0 @@ -47031,14 +62243,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "d503dee6f9b35a18", @@ -47052,10 +62264,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-18", "versions": 0 @@ -47076,12 +62288,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", "csv_to_tabular", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47102,12 +62314,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", "csv_to_tabular", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47128,9 +62340,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_sort_header_tool", "datamash_ops", - "tabular_to_csv", - "tp_sort_header_tool" + "tabular_to_csv" ], "update_time": "2023-05-18", "versions": 0 @@ -47172,12 +62384,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", "csv_to_tabular", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47198,12 +62410,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", "csv_to_tabular", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47224,11 +62436,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47249,11 +62461,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", "tabular_to_csv", - "csv_to_tabular", - "Filter1" + "csv_to_tabular" ], "update_time": "2023-05-18", "versions": 0 @@ -47274,11 +62486,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47299,12 +62511,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "tp_sort_header_tool", "Count1", - "datamash_ops", "tabular_to_csv", "csv_to_tabular", - "Filter1" + "datamash_ops" ], "update_time": "2023-05-18", "versions": 0 @@ -47314,14 +62526,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "762c64a9f588a420", @@ -47335,10 +62547,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47348,14 +62560,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "318be2b30bf7884c", @@ -47369,10 +62581,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47382,14 +62594,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "ae1ca223d6667070", @@ -47403,10 +62615,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47416,14 +62628,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "135e8888872e8413", @@ -47437,10 +62649,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47450,14 +62662,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "1842a61fe5f6965f", @@ -47471,10 +62683,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 2 @@ -47484,14 +62696,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "5b00ef046439d757", @@ -47505,10 +62717,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 0 @@ -47518,14 +62730,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "1ccc0c9e1c6821bb", @@ -47539,10 +62751,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47552,14 +62764,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "7baae0775071c7ec", @@ -47573,10 +62785,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47586,14 +62798,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "18c9095fbf5c4517", @@ -47607,10 +62819,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47620,14 +62832,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "ab8924d78fa5ef8f", @@ -47641,10 +62853,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47654,14 +62866,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "4dd7f6e1c1e7f96a", @@ -47675,10 +62887,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47688,14 +62900,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "fb18c5d14acb1b36", @@ -47709,10 +62921,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47722,14 +62934,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "487929c7b5be8dc3", @@ -47743,10 +62955,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47756,14 +62968,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "534b81d48df6b507", @@ -47777,10 +62989,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47790,14 +63002,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "b801e745205892f5", @@ -47811,10 +63023,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47824,14 +63036,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "fe8a1a970fd0d4cd", @@ -47845,10 +63057,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47858,14 +63070,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "cbc16cb5db98ab21", @@ -47879,10 +63091,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47892,14 +63104,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "f0ac222d3e965ab0", @@ -47913,10 +63125,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47926,14 +63138,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "98d4adf5774e274e", @@ -47947,10 +63159,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47960,14 +63172,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "b41ff6d8fb5a0878", @@ -47981,10 +63193,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-17", "versions": 1 @@ -47994,13 +63206,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Formatting", "Visualisation", + "Phylogenetic tree editing", + "Formatting", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "ed0ad728cf21702b", @@ -48015,14 +63227,14 @@ "asaim" ], "tools": [ - "metaphlan2krona", - "metaphlan2", + "export2graphlan", "graphlan_annotate", - "graphlan", - "format_metaphlan2_output", - "fastq_paired_end_interlacer", "taxonomy_krona_chart", - "export2graphlan" + "metaphlan2", + "fastq_paired_end_interlacer", + "graphlan", + "metaphlan2krona", + "format_metaphlan2_output" ], "update_time": "2023-05-17", "versions": 3 @@ -48032,14 +63244,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "3d5b39e454df584b", @@ -48053,10 +63265,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48077,10 +63289,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", "Filter1", "ggplot2_heatmap2", - "Cut1" + "Cut1", + "join1" ], "update_time": "2023-05-15", "versions": 2 @@ -48101,10 +63313,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", "Filter1", "ggplot2_heatmap2", - "Cut1" + "Cut1", + "join1" ], "update_time": "2023-05-15", "versions": 6 @@ -48114,14 +63326,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "71a9224fa6f3da9d", @@ -48135,10 +63347,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48148,14 +63360,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "c885eaabae612d6d", @@ -48169,10 +63381,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48193,10 +63405,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", "Filter1", "ggplot2_heatmap2", - "Cut1" + "Cut1", + "join1" ], "update_time": "2023-05-15", "versions": 3 @@ -48217,10 +63429,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", "Filter1", "ggplot2_heatmap2", - "Cut1" + "Cut1", + "join1" ], "update_time": "2023-05-15", "versions": 3 @@ -48230,14 +63442,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "9141c6449595c6a1", @@ -48251,10 +63463,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48264,14 +63476,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "f12fb4a95954c448", @@ -48285,10 +63497,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48309,10 +63521,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", "Filter1", "ggplot2_heatmap2", - "Cut1" + "Cut1", + "join1" ], "update_time": "2023-05-15", "versions": 1 @@ -48322,14 +63534,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "e62b659a5da9734e", @@ -48343,10 +63555,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48356,14 +63568,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "1be0c4adf13cf368", @@ -48377,10 +63589,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2023-05-15", "versions": 1 @@ -48390,11 +63602,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Data handling" ], "edam_topic": [], "id": "b26fee38f6f796d8", @@ -48438,22 +63650,22 @@ "name:single_cell" ], "tools": [ - "anndata_inspect", - "datamash_transpose", "regexColumn1", - "tp_cut_tool", - "Cut1", - "join1", - "monocle3_preprocess", - "monocle3_partition", - "monocle3_topmarkers", - "monocle3_learnGraph", - "monocle3_diffExp", - "monocle3_plotCells", "monocle3_orderCells", + "monocle3_diffExp", "Filter1", + "datamash_transpose", "monocle3_create", - "monocle3_reduceDim" + "monocle3_partition", + "monocle3_reduceDim", + "monocle3_topmarkers", + "monocle3_plotCells", + "monocle3_learnGraph", + "monocle3_preprocess", + "join1", + "tp_cut_tool", + "Cut1", + "anndata_inspect" ], "update_time": "2023-05-05", "versions": 30 @@ -48463,16 +63675,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "dadca1020f586338", @@ -48487,33 +63699,33 @@ "metagenomics" ], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_summary_single", + "mothur_cluster_split", + "mothur_count_seqs", "mothur_make_shared", "mothur_pre_cluster", - "mothur_summary_single", - "mothur_taxonomy_to_krona", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", - "mothur_align_seqs", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "XY_Plot_1" ], "update_time": "2023-04-27", @@ -48547,17 +63759,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "83049910e2cd5128", @@ -48572,21 +63784,21 @@ "variant-analysis" ], "tools": [ - "tp_easyjoin_tool", - "bwa_mem", - "bamleftalign", "samtools_calmd", - "trimmomatic", - "bg_column_arrange_by_header", "varscan_somatic", - "gemini_load", "samtools_rmdup", + "snpEff", + "gemini_load", + "trimmomatic", "gemini_query", "gemini_annotate", - "snpEff", "multiqc", + "tp_easyjoin_tool", + "bwa_mem", "fastqc", - "bamFilter" + "bamFilter", + "bg_column_arrange_by_header", + "bamleftalign" ], "update_time": "2023-04-17", "versions": 0 @@ -48596,29 +63808,29 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", + "Sequence motif recognition", + "Gene functional annotation", "Sequence assembly", - "Sequencing quality control", - "Formatting", - "Data retrieval", "Database search", - "Gene functional annotation", - "Protein feature detection", - "Sequence profile generation", + "Sequencing quality control", "Format validation", - "Sequence composition calculation", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence analysis", "Sequence database search", + "Sequence profile generation", "Sequence assembly validation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment", - "Sequence analysis", - "Validation" + "Sequence composition calculation", + "Sequence generation", + "Data retrieval", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "3eaa913306c16146", @@ -48631,18 +63843,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "interproscan", - "fasplit", - "tp_awk_tool", - "__FILTER_FROM_FILE__", - "kofamscan", - "tp_grep_tool", "fraggenescan", - "hmmer_hmmscan", "sort1", - "checkm_lineage_wf", + "kofamscan", "cat_bins", - "tp_cat" + "tp_cat", + "fasplit", + "checkm_lineage_wf", + "hmmer_hmmscan", + "interproscan", + "tp_grep_tool", + "__FILTER_FROM_FILE__", + "tp_awk_tool" ], "update_time": "2023-04-14", "versions": 13 @@ -48652,10 +63864,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Analysis", - "Sequence assembly", - "Read alignment" + "Read mapping", + "Read alignment", + "Sequence assembly" ], "edam_topic": [], "id": "3588c40cab9b4e1d", @@ -48679,29 +63891,29 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", + "Sequence motif recognition", + "Gene functional annotation", "Sequence assembly", - "Sequencing quality control", - "Formatting", - "Data retrieval", "Database search", - "Gene functional annotation", - "Protein feature detection", - "Sequence profile generation", + "Sequencing quality control", "Format validation", - "Sequence composition calculation", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence analysis", "Sequence database search", + "Sequence profile generation", "Sequence assembly validation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment", - "Sequence analysis", - "Validation" + "Sequence composition calculation", + "Sequence generation", + "Data retrieval", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "6416cfdbd5273063", @@ -48714,18 +63926,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "interproscan", - "fasplit", - "tp_awk_tool", - "__FILTER_FROM_FILE__", - "kofamscan", - "tp_grep_tool", "fraggenescan", - "hmmer_hmmscan", "sort1", - "checkm_lineage_wf", + "kofamscan", "cat_bins", - "tp_cat" + "tp_cat", + "fasplit", + "checkm_lineage_wf", + "hmmer_hmmscan", + "interproscan", + "tp_grep_tool", + "__FILTER_FROM_FILE__", + "tp_awk_tool" ], "update_time": "2023-04-12", "versions": 1 @@ -48749,11 +63961,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2023-04-11", "versions": 1 @@ -48763,19 +63975,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "De-novo assembly", + "Genome assembly", "Sequence alignment", - "Phasing", - "k-mer counting", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", - "Genome assembly", - "Sequence trimming", "Genotyping", - "Transcriptome assembly" + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence alignment analysis", + "Sequence trimming", + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "bc32937d505135ab", @@ -48788,26 +64000,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bandage_image", + "smudgeplot", + "collapse_dataset", + "tp_find_and_replace", "bg_diamond", + "bwa_mem2", "blobtoolkit", "gfastats", - "meryl", - "pretext_map", - "tp_find_and_replace", - "hisat2", "pretext_snapshot", + "busco", + "genomescope", + "bg_diamond_makedb", + "merqury", + "meryl", + "bandage_image", "jellyfish", "CONVERTER_gz_to_uncompressed", + "pretext_map", + "hisat2", "bellerophon", - "bg_diamond_makedb", - "collapse_dataset", - "interactive_tool_blobtoolkit", - "busco", - "bwa_mem2", - "genomescope", - "smudgeplot", - "merqury" + "interactive_tool_blobtoolkit" ], "update_time": "2023-04-03", "versions": 17 @@ -48828,9 +64040,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastq_to_fasta_python", + "fastq_stats", "cshl_fastx_reverse_complement", - "fastq_stats" + "fastq_to_fasta_python" ], "update_time": "2023-03-29", "versions": 1 @@ -48840,15 +64052,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", "Sequence alignment", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", + "De-novo assembly", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3069c17b52decab4", @@ -48861,17 +64073,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "meryl", + "blobtoolkit", "collapse_dataset", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "interactive_tool_blobtoolkit", "merqury", - "hisat2", + "meryl", + "gfastats", + "interactive_tool_blobtoolkit", "busco", "genomescope", - "ncbi_blastn_wrapper", - "blobtoolkit", - "gfastats" + "hisat2" ], "update_time": "2023-03-27", "versions": 16 @@ -48896,9 +64108,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-03-23", "versions": 1 @@ -48927,8 +64139,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-03-23", @@ -48968,14 +64180,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "96d198ed953449fd", @@ -49000,34 +64212,34 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", - "Sequence assembly", - "Coding region prediction", - "Sequencing quality control", - "Formatting", "Visualisation", - "Data retrieval", - "Read pre-processing", - "Sequence trimming", - "Database search", + "Sequence motif recognition", "Gene functional annotation", - "Protein feature detection", - "Sequence profile generation", + "Sequence assembly", + "Database search", + "Primer removal", + "Sequencing quality control", "Format validation", - "Sequence composition calculation", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence analysis", "Sequence database search", - "Local alignment", + "Sequence trimming", "Sequence assembly validation", + "Sequence profile generation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", - "Primer removal", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment", - "Sequence analysis", - "Validation" + "Local alignment", + "Read pre-processing", + "Sequence composition calculation", + "Sequence generation", + "Data retrieval", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "6158c3b5fc12044e", @@ -49042,23 +64254,23 @@ "name:microgalaxy" ], "tools": [ - "interproscan", - "fasplit", - "tp_awk_tool", - "maxbin2", - "trim_galore", - "quast", - "kofamscan", - "tp_grep_tool", "fraggenescan", - "hmmer_hmmscan", "sort1", - "fastqc", + "kofamscan", + "coverm_contig", + "cat_bins", + "trim_galore", "coverm_genome", + "tp_cat", + "fasplit", "checkm_lineage_wf", - "cat_bins", - "coverm_contig", - "tp_cat" + "hmmer_hmmscan", + "quast", + "fastqc", + "interproscan", + "maxbin2", + "tp_grep_tool", + "tp_awk_tool" ], "update_time": "2023-03-16", "versions": 22 @@ -49079,11 +64291,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ecology_stat_presence_abs", "tool_anonymization", + "ecology_beta_diversity", "ecology_presence_abs_abund", "ecology_link_between_var", - "ecology_stat_presence_abs", - "ecology_beta_diversity", "ecology_homogeneity_normality" ], "update_time": "2023-03-13", @@ -49094,11 +64306,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", "Sequence contamination filtering", - "Primer removal", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -49113,9 +64325,9 @@ "tags": [], "tools": [ "fastq_join", + "cutadapt", "fastp", - "bg_diamond", - "cutadapt" + "bg_diamond" ], "update_time": "2023-03-12", "versions": 1 @@ -49127,14 +64339,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "9e01e24c5e749365", @@ -49147,10 +64359,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "hisat2", + "trimmomatic", "fastqc", + "hisat2", "deseq2" ], "update_time": "2023-03-07", @@ -49165,20 +64377,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "03be9d62e8e4a129", @@ -49194,22 +64406,22 @@ "pag2023" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-03-03", "versions": 1 @@ -49222,17 +64434,17 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Local alignment", - "Sequence alignment", + "Generation", "Genome indexing", - "Sequence contamination filtering", - "Global alignment", + "Sequence alignment analysis", "Sequence analysis", - "Generation", - "Validation" + "Global alignment", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "b77e3b08092fa73e", @@ -49248,31 +64460,31 @@ "virology" ], "tools": [ - "samtools_view", - "fastp", "samtools_merge", - "ivar_consensus", - "split_file_to_collection", - "tp_sed_tool", - "EMBOSS: maskseq51", - "datamash_ops", - "samtools_stats", - "__ZIP_COLLECTION__", - "__FILTER_FAILED_DATASETS__", - "param_value_from_file", - "compose_text_param", - "__SORTLIST__", + "Cut1", + "tp_cat", + "Grep1", "__APPLY_RULES__", "qualimap_bamqc", - "__FLATTEN__", - "fasta_compute_length", - "ivar_trim", - "bwa_mem", "collection_element_identifiers", - "Cut1", + "param_value_from_file", + "EMBOSS: maskseq51", "multiqc", - "Grep1", - "tp_cat" + "__SORTLIST__", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "fasta_compute_length", + "compose_text_param", + "ivar_consensus", + "__ZIP_COLLECTION__", + "samtools_stats", + "fastp", + "__FILTER_FAILED_DATASETS__", + "split_file_to_collection", + "tp_sed_tool", + "datamash_ops" ], "update_time": "2023-03-02", "versions": 1 @@ -49282,16 +64494,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Gene expression profiling", + "Statistical calculation", + "Primer removal", "Sequencing quality control", "Sequence comparison", - "Primer removal", + "Sequence similarity search", "Read pre-processing", + "Sequence composition calculation", + "Sequence alignment analysis", "Sequence trimming", - "Statistical calculation" + "Gene expression profiling" ], "edam_topic": [], "id": "385cc7df70d7916b", @@ -49306,12 +64518,12 @@ "name:microgalaxy" ], "tools": [ + "kallisto_quant", "bg_sortmerna", "trim_galore", - "__UNZIP_COLLECTION__", - "kallisto_quant", "collection_column_join", - "fastqc" + "fastqc", + "__UNZIP_COLLECTION__" ], "update_time": "2023-02-27", "versions": 16 @@ -49334,10 +64546,10 @@ "variant-analysis" ], "tools": [ - "bcftools_norm", "regexColumn1", "bcftools_merge", "Filter1", + "bcftools_norm", "CONVERTER_gz_to_uncompressed" ], "update_time": "2023-02-25", @@ -49350,17 +64562,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f5005e80d9ffa109", @@ -49375,15 +64587,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-02-23", "versions": 1 @@ -49426,31 +64638,31 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_ops", - "bg_column_arrange_by_header", - "scanpy_read_10x", - "scanpy_multiplet_scrublet", - "__BUILD_LIST__", + "scanpy_find_markers", "scanpy_filter_genes", - "scanpy_run_umap", - "scanpy_parameter_iterator", - "__MERGE_COLLECTION__", - "tp_replace_in_line", - "scanpy_integrate_harmony", - "scanpy_find_variable_genes", - "__FILTER_FAILED_DATASETS__", + "bg_column_arrange_by_header", "join1", + "scanpy_plot_scrublet", + "scanpy_normalise_data", "scanpy_compute_graph", + "scanpy_integrate_harmony", + "__MERGE_COLLECTION__", + "__BUILD_LIST__", + "scanpy_find_variable_genes", + "scanpy_filter_cells", + "scanpy_run_umap", "scanpy_run_tsne", - "scanpy_find_markers", - "scanpy_find_cluster", - "scanpy_scale_data", + "tp_replace_in_line", "scanpy_run_pca", - "Cut1", - "scanpy_plot_scrublet", + "scanpy_find_cluster", + "scanpy_read_10x", + "anndata_ops", + "scanpy_parameter_iterator", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "scanpy_normalise_data", - "scanpy_filter_cells" + "scanpy_multiplet_scrublet", + "Cut1", + "scanpy_scale_data" ], "update_time": "2023-02-17", "versions": 1 @@ -49462,22 +64674,22 @@ ], "doi": "", "edam_operation": [ + "Genome annotation", + "Sequence contamination filtering", + "Visualisation", + "Sequencing quality control", "Aggregation", "Coding region prediction", - "Sequencing quality control", - "Phylogenetic analysis", - "Variant calling", - "Phylogenetic tree generation", + "Sequence analysis", "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", "Gene prediction", + "Phylogenetic tree generation", "Genome assembly", - "Genome annotation", - "Phylogenetic tree visualisation", - "Sequence analysis", + "Phylogenetic analysis", + "Variant calling", "Validation", + "Phylogenetic tree visualisation", + "Antimicrobial resistance prediction", "Taxonomic classification" ], "edam_topic": [], @@ -49496,23 +64708,23 @@ "pathogen" ], "tools": [ - "roary", + "prokka", + "kraken2", + "krakentools_kreport2krona", "abricate", + "fastp", + "multiqc", + "taxonomy_krona_chart", "snippy_core", "abricate_summary", - "kraken2", + "roary", "sistr_cmd", - "snippy", "quast", - "snp_dists", - "taxonomy_krona_chart", - "fastp", "iqtree", - "shovill", - "prokka", - "multiqc", + "snippy", + "snp_dists", "staramr_search", - "krakentools_kreport2krona" + "shovill" ], "update_time": "2023-02-12", "versions": 1 @@ -49524,21 +64736,21 @@ ], "doi": "", "edam_operation": [ - "Coding region prediction", + "Genome annotation", + "Sequence contamination filtering", + "Visualisation", "Sequencing quality control", - "Phylogenetic analysis", - "Variant calling", - "Phylogenetic tree generation", + "Coding region prediction", + "Sequence analysis", "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", "Gene prediction", + "Phylogenetic tree generation", "Genome assembly", - "Genome annotation", - "Phylogenetic tree visualisation", - "Sequence analysis", + "Phylogenetic analysis", + "Variant calling", "Validation", + "Phylogenetic tree visualisation", + "Antimicrobial resistance prediction", "Taxonomic classification" ], "edam_topic": [], @@ -49557,23 +64769,23 @@ "workflow" ], "tools": [ - "roary", - "abricate", "Kraken2Tax", - "snippy_core", + "prokka", "kraken2", - "sistr_cmd", + "abricate", + "fastp", + "multiqc", + "taxonomy_krona_chart", + "snippy_core", "abricate_summary", - "snippy", + "roary", + "sistr_cmd", "quast", - "snp_dists", - "taxonomy_krona_chart", - "fastp", "iqtree", - "shovill", - "prokka", - "multiqc", - "staramr_search" + "snippy", + "snp_dists", + "staramr_search", + "shovill" ], "update_time": "2023-02-12", "versions": 1 @@ -49583,8 +64795,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence comparison", "Protein sequence analysis", + "Sequence comparison", "Sequence analysis" ], "edam_topic": [], @@ -49599,11 +64811,11 @@ "tags": [], "tools": [ "cat1", - "pfamscan", - "tp_awk_tool", - "cpat", "isoformswitchanalyzer", - "Remove beginning1" + "Remove beginning1", + "cpat", + "tp_awk_tool", + "pfamscan" ], "update_time": "2023-02-11", "versions": 16 @@ -49613,16 +64825,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Sequence assembly validation", - "Visualisation", "Sequence contamination filtering", + "Visualisation", "Statistical calculation", "Genome assembly", - "Validation" + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", + "Sequence assembly validation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "1860e02bcb894a64", @@ -49637,21 +64849,21 @@ "genome-assembly" ], "tools": [ - "ncbi_blastx_wrapper", - "fasta_merge_files_and_filter_unique_sequences", - "fasta_filter_by_length", + "bwa_mem2", + "bowtie2", + "ncbi_makeblastdb", + "spades_rnaviralspades", "collapse_dataset", "samtools_fastx", - "samtools_view", - "quast", + "ncbi_blastx_wrapper", + "ncbi_blastn_wrapper", "fastp", "multiqc", - "ncbi_makeblastdb", - "bwa_mem2", + "quast", "fastqc", - "ncbi_blastn_wrapper", - "bowtie2", - "spades_rnaviralspades" + "fasta_filter_by_length", + "fasta_merge_files_and_filter_unique_sequences", + "samtools_view" ], "update_time": "2023-02-10", "versions": 27 @@ -49678,9 +64890,9 @@ "name:rna-seq" ], "tools": [ - "fastq_groomer", + "bowtie2", "rseqc_infer_experiment", - "bowtie2" + "fastq_groomer" ], "update_time": "2023-02-10", "versions": 3 @@ -49690,27 +64902,27 @@ "creators": [], "doi": "", "edam_operation": [ + "Genome annotation", + "Sequence contamination filtering", + "Sequence alignment", + "Primer removal", "Sequencing quality control", - "Differential gene expression analysis", "Formatting", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", - "Read pre-processing", - "Sequence clustering", + "Coding region prediction", "Sequence trimming", - "Genome indexing", - "Generation", - "Sequence composition calculation", "Read mapping", - "Variant calling", - "Sequence alignment", "Gene prediction", - "Genome annotation", - "Primer removal", "Statistical calculation", - "Taxonomic classification", - "Coding region prediction", - "Validation" + "Sequence clustering", + "Differential gene expression analysis", + "Sequence composition calculation", + "Read pre-processing", + "Generation", + "Genome indexing", + "Variant calling", + "Validation", + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "6a5c39c1d38a10c2", @@ -49723,25 +64935,25 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", - "prokka", - "fastqc", "abricate", - "metaphlan2krona", - "vcffilter2", "bismark_deduplicate", - "gatk_count_covariates", - "freebayes", - "antismash", - "bamleftalign", - "ngsutils_bam_filter", + "metaphlan2krona", "krona-text", + "fastqc", + "bismark_pretty_report", + "prokka", + "ngsutils_bam_filter", + "multiqc", + "vcffilter2", "bwa_mem", + "bamleftalign", "kraken2", - "bcftools_consensus", + "antismash", + "trim_galore", "bismark_bowtie2", - "multiqc", - "bismark_pretty_report" + "bcftools_consensus", + "freebayes", + "gatk_count_covariates" ], "update_time": "2023-02-08", "versions": 8 @@ -49762,15 +64974,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", - "anndata_manipulate", - "anndata_ops", - "Cut1", + "Paste1", "scanpy_read_10x", + "retrieve_scxa", + "anndata_ops", + "anndata_manipulate", "sceasy_convert", - "Paste1", "tp_replace_in_column", - "retrieve_scxa" + "Cut1", + "anndata_inspect" ], "update_time": "2023-02-08", "versions": 1 @@ -49780,9 +64992,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "df455b86fff16116", @@ -49795,15 +65007,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2023-02-08", "versions": 1 @@ -49826,24 +65038,24 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "anndata_manipulate", - "anndata_ops", - "join1", "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "anndata_manipulate", + "anndata_ops", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2023-02-08", "versions": 0 @@ -49871,9 +65083,9 @@ "pag2023" ], "tools": [ - "gfastats", "param_value_from_file", - "bionano_scaffold" + "bionano_scaffold", + "gfastats" ], "update_time": "2023-02-07", "versions": 1 @@ -49883,9 +65095,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "f39528391f22aab0", @@ -49898,9 +65110,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "fastq_filter", - "fastq_groomer" + "fastq_groomer", + "fastqc" ], "update_time": "2023-02-06", "versions": 1 @@ -49928,9 +65140,9 @@ "vgp_curated" ], "tools": [ - "gfastats", "param_value_from_file", - "bionano_scaffold" + "bionano_scaffold", + "gfastats" ], "update_time": "2023-02-03", "versions": 9 @@ -49959,14 +65171,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-02-02", "versions": 1 @@ -49979,13 +65191,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -50001,19 +65213,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", - "bedtools_bamtobed", + "bwa_mem2", + "param_value_from_file", + "sort1", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "param_value_from_file", - "yahs", - "sort1", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-02-02", "versions": 19 @@ -50023,16 +65235,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequencing quality control", - "Formatting", "Sequence alignment", - "Read summarisation", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "a461ea397418f3aa", @@ -50045,13 +65257,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "picard_MarkDuplicates", - "rna_star", - "fastq_dump", "featurecounts", - "collection_column_join", "multiqc", - "cutadapt" + "collection_column_join", + "rna_star", + "cutadapt", + "fastq_dump", + "picard_MarkDuplicates" ], "update_time": "2023-02-01", "versions": 4 @@ -50067,14 +65279,14 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Sequence composition calculation", + "Validation", + "Taxonomic classification" ], "edam_topic": [], "id": "57d3109f32defa3b", @@ -50090,14 +65302,14 @@ "nanopore" ], "tools": [ - "seq_filter_by_id", - "kraken2", - "porechop", - "nanoplot", "filter_tabular", + "kraken2", "fastp", "multiqc", - "fastqc" + "nanoplot", + "porechop", + "fastqc", + "seq_filter_by_id" ], "update_time": "2023-01-29", "versions": 71 @@ -50109,9 +65321,9 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "5436eb1c430a38dd", @@ -50124,9 +65336,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "novoplasty", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2023-01-27", "versions": 2 @@ -50139,16 +65351,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "a3f082ff30357040", @@ -50164,16 +65376,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-01-26", "versions": 24 @@ -50205,19 +65417,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f6a625946dea60fa", @@ -50232,19 +65444,19 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "merqury", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-01-20", "versions": 6 @@ -50254,11 +65466,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "23821870734575e9", @@ -50271,9 +65483,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", + "rna_star", "multiqc", - "rna_star" + "fastqc" ], "update_time": "2023-01-19", "versions": 3 @@ -50285,15 +65497,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "ef1d11b79a2e1727", @@ -50308,18 +65520,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -50331,15 +65543,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "d3494c6124f820b2", @@ -50354,18 +65566,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -50377,15 +65589,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "86e2e2faa2e0bd46", @@ -50400,17 +65612,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -50422,15 +65634,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b323867a9efcc6c6", @@ -50445,13 +65657,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -50463,19 +65675,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "25aa944237d7fb82", @@ -50490,23 +65702,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -50518,19 +65730,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c3eba26c5d7febff", @@ -50545,23 +65757,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -50573,15 +65785,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b9ad204395f7d931", @@ -50596,13 +65808,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -50615,17 +65827,17 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "19bb57f8cfa48bb9", @@ -50640,18 +65852,18 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-01-18", "versions": 12 @@ -50678,8 +65890,8 @@ "pag2023" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-01-17", "versions": 0 @@ -50692,19 +65904,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "2e418c5810012e5a", @@ -50720,19 +65932,19 @@ "pag2023" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "merqury", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-01-17", "versions": 0 @@ -50745,12 +65957,12 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", + "Genome assembly", + "Sequence alignment", "Data handling", + "Sequence assembly validation", "Scaffolding", - "Genome assembly", "Mapping", - "Sequence alignment", "Transcriptome assembly" ], "edam_topic": [], @@ -50766,17 +65978,17 @@ "pag2023" ], "tools": [ - "bellerophon", - "bedtools_bamtobed", - "__EXTRACT_DATASET__", - "pretext_map", + "bwa_mem2", "param_value_from_file", - "yahs", "sort1", - "busco", - "bwa_mem2", + "__EXTRACT_DATASET__", + "yahs", + "gfastats", "pretext_snapshot", - "gfastats" + "bedtools_bamtobed", + "busco", + "pretext_map", + "bellerophon" ], "update_time": "2023-01-17", "versions": 2 @@ -50786,16 +65998,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "533819bcb5aa78c5", @@ -50808,15 +66020,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2023-01-16", "versions": 0 @@ -50830,20 +66042,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "085c3a4c89d137b5", @@ -50858,22 +66070,22 @@ "vgp_curated" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-01-09", "versions": 7 @@ -50899,8 +66111,8 @@ "vgp_curated" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-01-09", "versions": 16 @@ -50926,8 +66138,8 @@ "vgp_curated" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-01-09", "versions": 3 @@ -50937,14 +66149,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", "Sequencing quality control", "Gene regulatory network analysis", - "Mapping", "Differential binding analysis", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7d44ea091d437edf", @@ -50962,34 +66174,34 @@ "name:chip-seq" ], "tools": [ + "deeptools_plot_correlation", + "samtool_filter2", + "chipseeker", "gops_concat_1", + "gops_subtract_1", + "deeptools_bam_compare", + "deeptools_bigwig_compare", + "bowtie2", + "Filter1", "deeptools_multi_bam_summary", - "bedtools_slopbed", + "deeptools_plot_heatmap", + "multiqc", + "gops_cluster_1", "deeptools_compute_matrix", - "deeptools_plot_correlation", - "macs2_callpeak", - "deeptools_bigwig_compare", "addValue", - "deeptools_bam_compare", - "chipseeker", - "tp_replace_in_column", - "deeptools_plot_heatmap", - "ggplot2_heatmap2", - "cat1", - "gops_subtract_1", "samtools_flagstat", - "deeptools_plot_fingerprint", + "macs2_callpeak", + "cat1", "diffbind", - "gops_cluster_1", - "samtool_filter2", - "Remove beginning1", + "bedtools_mergebed", + "deeptools_plot_fingerprint", "bedtools_sortbed", - "multiqc", - "Filter1", - "bowtie2", - "deeptools_plot_coverage", + "tp_replace_in_column", + "bedtools_slopbed", "bedtools_intersectbed", - "bedtools_mergebed" + "deeptools_plot_coverage", + "Remove beginning1", + "ggplot2_heatmap2" ], "update_time": "2023-01-09", "versions": 0 @@ -50999,9 +66211,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Visualisation", - "Sequencing quality control", "Sequence contamination filtering", + "Sequencing quality control", + "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -51015,8 +66227,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "taxonomy_krona_chart", "fastp", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2023-01-05", @@ -51049,16 +66261,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "591ebf913450f49e", @@ -51071,15 +66283,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2022-12-21", "versions": 5 @@ -51089,16 +66301,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5e3c352233aa7a52", @@ -51111,14 +66323,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2022-12-21", "versions": 2 @@ -51128,16 +66340,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "99799eec4497f977", @@ -51150,15 +66362,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2022-12-21", "versions": 3 @@ -51195,9 +66407,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "c2f0decb06f0bb90", @@ -51214,8 +66426,8 @@ "name:qc" ], "tools": [ - "multiqc", - "fastp" + "fastp", + "multiqc" ], "update_time": "2022-12-12", "versions": 9 @@ -51225,10 +66437,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence analysis", "Scatter plot plotting", "Antimicrobial resistance prediction", "Structural variation detection", - "Sequence analysis", "Box-Whisker plot plotting" ], "edam_topic": [], @@ -51242,13 +66454,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "filter_tabular", + "PlasFlow", "abricate", - "fasta_merge_files_and_filter_unique_sequences", - "ncbi_acc_download", "nanoplot", - "PlasFlow", "isescan", - "filter_tabular" + "ncbi_acc_download", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2022-12-09", "versions": 7 @@ -51271,12 +66483,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "spring_model_all", - "__FILTER_FAILED_DATASETS__", - "hhsearch", "collection_element_identifiers", "rbc_splitfasta", + "__FILTER_FAILED_DATASETS__", + "hhsearch", "ffindex_dbkit_merge", + "spring_model_all", "ffindex_dbkit_create", "spring_minz" ], @@ -51301,11 +66513,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "spring_model_all", - "__FILTER_FAILED_DATASETS__", - "hhsearch", "collection_element_identifiers", "rbc_splitfasta", + "__FILTER_FAILED_DATASETS__", + "hhsearch", + "spring_model_all", "ffindex_dbkit_create", "spring_minz" ], @@ -51317,12 +66529,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Sequencing quality control", + "Validation", "Sequence alignment", - "Validation" + "Sequence trimming", + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "c2d814f2182c0082", @@ -51335,9 +66547,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "multiqc", "rna_star", - "cutadapt" + "cutadapt", + "multiqc" ], "update_time": "2022-12-08", "versions": 7 @@ -51370,16 +66582,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Validation" ], "edam_topic": [], "id": "29a855d928337f8f", @@ -51393,11 +66605,11 @@ "tags": [], "tools": [ "featurecounts", - "hisat2", + "cutadapt", "multiqc", "collection_column_join", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2022-12-06", "versions": 0 @@ -51407,16 +66619,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Validation" ], "edam_topic": [], "id": "300301c23327f797", @@ -51430,11 +66642,11 @@ "tags": [], "tools": [ "featurecounts", - "hisat2", + "cutadapt", "multiqc", "collection_column_join", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2022-12-06", "versions": 0 @@ -51478,12 +66690,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "generic_filter", - "normalization", "intens_check", - "Batch_correction", + "normalization", + "generic_filter", + "Multivariate", "quality_metrics", - "Multivariate" + "Batch_correction" ], "update_time": "2022-12-05", "versions": 0 @@ -51493,17 +66705,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Genome assembly", - "Multilocus sequence typing", - "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", - "Sequence contamination filtering", "Gene prediction", "Genome annotation", + "Sequence contamination filtering", + "Visualisation", + "Genome assembly", + "Multilocus sequence typing", + "Sequencing quality control", "Coding region prediction", - "Validation" + "Sequence assembly validation", + "Validation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "37da7b42cb063a3a", @@ -51520,14 +66732,14 @@ "genome" ], "tools": [ + "prokka", + "spades", "abricate", - "abricate_summary", - "mlst", - "quast", "fastp", - "prokka", "multiqc", - "spades" + "abricate_summary", + "quast", + "mlst" ], "update_time": "2022-12-03", "versions": 18 @@ -51539,15 +66751,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "c98a14fcf5998159", @@ -51562,18 +66774,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -51585,15 +66797,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "a3da32b6b45da639", @@ -51608,17 +66820,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -51630,15 +66842,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c7a8f7aabc219831", @@ -51653,13 +66865,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -51671,19 +66883,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "3b8ef7905c902b27", @@ -51698,23 +66910,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -51726,15 +66938,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "55ead91471bf1008", @@ -51749,13 +66961,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -51767,17 +66979,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "cfe47f0c78ed5ec4", @@ -51792,15 +67004,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -51823,11 +67035,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -51850,11 +67062,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -51877,11 +67089,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 2 @@ -51904,11 +67116,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 2 @@ -51931,11 +67143,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 3 @@ -51958,11 +67170,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -51985,11 +67197,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 4 @@ -52012,11 +67224,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 3 @@ -52039,11 +67251,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -52066,11 +67278,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 3 @@ -52093,11 +67305,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -52120,11 +67332,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 1 @@ -52147,11 +67359,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-29", "versions": 2 @@ -52177,10 +67389,10 @@ "deconvolution" ], "tools": [ - "tp_easyjoin_tool", - "Cut1", "table_compute", - "Count1" + "Cut1", + "Count1", + "tp_easyjoin_tool" ], "update_time": "2022-11-29", "versions": 33 @@ -52203,17 +67415,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_multijoin_tool", + "ggplot2_heatmap", + "plotly_regression_performance_plots", "Add_a_column1", "datamash_transpose", + "ggplot2_violin", "table_compute", - "tp_awk_tool", + "tp_multijoin_tool", + "datamash_reverse", "Cut1", - "ggplot2_violin", - "plotly_regression_performance_plots", "addValue", - "ggplot2_heatmap", - "datamash_reverse" + "tp_awk_tool" ], "update_time": "2022-11-27", "versions": 1 @@ -52234,14 +67446,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_multijoin_tool", + "sort1", "datamash_transpose", + "Show beginning1", + "tp_multijoin_tool", "tp_cut_tool", + "music_deconvolution", "add_line_to_file", - "sort1", - "Show beginning1", - "music_construct_eset", - "music_deconvolution" + "music_construct_eset" ], "update_time": "2022-11-25", "versions": 2 @@ -52271,17 +67483,17 @@ "name:single-cell" ], "tools": [ + "tp_find_and_replace", "table_compute", - "bg_column_arrange_by_header", + "Grep1", + "Remove beginning1", "Count1", - "join1", - "tp_find_and_replace", - "Cut1", - "tp_awk_tool", "tp_sed_tool", - "Remove beginning1", + "join1", + "bg_column_arrange_by_header", "annotatemyids", - "Grep1" + "Cut1", + "tp_awk_tool" ], "update_time": "2022-11-24", "versions": 6 @@ -52291,11 +67503,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly", - "Mapping", "Pairwise sequence alignment", + "Sequence assembly", "Variant calling", - "Base-calling" + "Base-calling", + "Mapping" ], "edam_topic": [], "id": "70d3ebf31940bfb3", @@ -52309,9 +67521,9 @@ "tags": [], "tools": [ "minimap2", + "bedtools_genomecoveragebed", "medaka_consensus", - "porechop", - "bedtools_genomecoveragebed" + "porechop" ], "update_time": "2022-11-23", "versions": 6 @@ -52325,20 +67537,20 @@ ], "doi": "", "edam_operation": [ - "Filtering", + "Sequence contamination filtering", + "Visualisation", + "Sequence alignment", + "SNP detection", "Genome alignment", - "Read mapping", - "Generation", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Visualisation", - "Sequence contamination filtering", - "Taxonomic classification", + "Generation", "Genome indexing", - "SNP detection", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Read mapping", + "Filtering", + "Taxonomic classification" ], "edam_topic": [], "id": "4a764275d4bf9f31", @@ -52351,24 +67563,24 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "lofreq_filter", - "bwa_mem", - "samtools_depth", - "Kraken2Tax", - "picard_MarkDuplicates", + "samtools_stats", + "freyja_aggregate_plot", "kraken2", + "lofreq_viterbi", "snpeff_sars_cov_2", - "read_it_and_keep", - "samtools_view", - "samtools_stats", - "taxonomy_krona_chart", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", - "freyja_aggregate_plot", + "taxonomy_krona_chart", "multiqc", - "freyja_demix" + "samtools_depth", + "picard_MarkDuplicates", + "lofreq_indelqual", + "freyja_demix", + "bwa_mem", + "lofreq_call", + "samtools_view", + "read_it_and_keep", + "Kraken2Tax" ], "update_time": "2022-11-22", "versions": 9 @@ -52382,18 +67594,18 @@ ], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Filtering", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Visualisation", "Sequence contamination filtering", + "Visualisation", + "Sequence alignment", "Genome alignment", - "Genome indexing", + "Sequencing quality control", "Generation", + "Genome indexing", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Read mapping", + "Filtering", + "Taxonomic classification" ], "edam_topic": [], "id": "d88145e7475e0b7b", @@ -52406,28 +67618,28 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Kraken2Tax", - "samtools_view", - "taxonomy_krona_chart", - "fastp", + "collapse_dataset", + "cooc_tabmut", + "freyja_demix", "lofreq_call", + "qualimap_bamqc", + "multiqc", "lofreq_indelqual", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "kraken2", + "lofreq_viterbi", + "taxonomy_krona_chart", "cooc_mutbamscan", "read_it_and_keep", + "Kraken2Tax", "samtools_stats", - "freyja_demix", - "samtools_depth", - "__FILTER_FAILED_DATASETS__", - "collapse_dataset", "freyja_aggregate_plot", - "qualimap_bamqc", - "__FLATTEN__", - "ivar_trim", - "bwa_mem", - "kraken2", - "cooc_tabmut", - "lofreq_viterbi", - "multiqc" + "fastp", + "__FILTER_FAILED_DATASETS__", + "samtools_depth" ], "update_time": "2022-11-22", "versions": 33 @@ -52437,11 +67649,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -52455,11 +67667,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", + "trim_galore", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2022-11-21", @@ -52485,12 +67697,12 @@ "aiv" ], "tools": [ - "Cut1", "tp_find_and_replace", - "samtools_view", - "__RELABEL_FROM_FILE__", + "Grep1", "split_file_to_collection", - "Grep1" + "Cut1", + "__RELABEL_FROM_FILE__", + "samtools_view" ], "update_time": "2022-11-19", "versions": 3 @@ -52513,11 +67725,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-17", "versions": 1 @@ -52559,11 +67771,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-17", "versions": 2 @@ -52586,11 +67798,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-17", "versions": 3 @@ -52613,11 +67825,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-15", "versions": 3 @@ -52670,13 +67882,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", + "sort1", "table_compute", - "tp_awk_tool", - "tp_cut_tool", "tp_sed_tool", - "sort1", - "annotatemyids" + "tp_easyjoin_tool", + "tp_cut_tool", + "annotatemyids", + "tp_awk_tool" ], "update_time": "2022-11-14", "versions": 3 @@ -52701,8 +67913,8 @@ "tags": [], "tools": [ "taxonomy_krona_chart", - "Kraken2Tax", - "kraken2" + "kraken2", + "Kraken2Tax" ], "update_time": "2022-11-13", "versions": 2 @@ -52727,8 +67939,8 @@ "tags": [], "tools": [ "taxonomy_krona_chart", - "Kraken2Tax", - "kraken2" + "kraken2", + "Kraken2Tax" ], "update_time": "2022-11-13", "versions": 2 @@ -52758,10 +67970,10 @@ "name:single-cell" ], "tools": [ + "regex1", + "music_manipulate_eset", "column_remove_by_header", "tp_cut_tool", - "music_manipulate_eset", - "regex1", "annotatemyids", "music_construct_eset" ], @@ -52793,13 +68005,13 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", "datamash_transpose", - "music_manipulate_eset", "scanpy_read_10x", + "retrieve_scxa", + "music_manipulate_eset", "annotatemyids", - "music_construct_eset", - "retrieve_scxa" + "anndata_inspect", + "music_construct_eset" ], "update_time": "2022-11-12", "versions": 1 @@ -52828,12 +68040,12 @@ "name:single-cell" ], "tools": [ - "tp_cut_tool", + "regex1", + "retrieve_scxa", "join1", + "tp_cut_tool", "Cut1", - "regex1", - "add_line_to_file", - "retrieve_scxa" + "add_line_to_file" ], "update_time": "2022-11-12", "versions": 1 @@ -52861,17 +68073,17 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", "cat1", - "tp_easyjoin_tool", - "table_compute", - "anndata_manipulate", + "sort1", "scanpy_plot", + "anndata_manipulate", "scanpy_inspect", - "scanpy_regress_variable", + "table_compute", + "addValue", + "tp_easyjoin_tool", "scanpy_cluster_reduce_dimension", - "sort1", - "addValue" + "scanpy_regress_variable", + "anndata_inspect" ], "update_time": "2022-11-10", "versions": 6 @@ -52882,9 +68094,9 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", "Phylogenetic tree generation", - "Genome visualisation" + "Genome visualisation", + "Variant calling" ], "edam_topic": [], "id": "920aab45ff028ed4", @@ -52910,9 +68122,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", "Validation", + "Sequencing quality control", "Genome assembly" ], "edam_topic": [], @@ -52926,8 +68138,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "multiqc", "fastp", + "multiqc", "shovill" ], "update_time": "2022-11-09", @@ -52940,15 +68152,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "fa53b172def3fe75", @@ -52963,18 +68175,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-11-03", "versions": 1 @@ -52995,14 +68207,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "Filter1", - "Grep1" + "fasta_cli", + "Cut1", + "peptide_shaker" ], "update_time": "2022-10-28", "versions": 2 @@ -53014,15 +68226,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c6ca9e6fd28979f8", @@ -53037,13 +68249,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-10-27", "versions": 1 @@ -53055,19 +68267,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "48f63ef14a12f306", @@ -53082,23 +68294,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-10-27", "versions": 1 @@ -53126,17 +68338,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-10-27", "versions": 1 @@ -53157,14 +68369,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "table_compute", - "keras_model_config", - "column_remove_by_header", - "ml_visualization_ex", "model_prediction", - "Remove beginning1", + "column_remove_by_header", + "table_compute", "keras_train_and_eval", - "keras_model_builder" + "Remove beginning1", + "keras_model_config", + "keras_model_builder", + "ml_visualization_ex" ], "update_time": "2022-10-24", "versions": 35 @@ -53190,20 +68402,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-10-20", "versions": 1 @@ -53224,10 +68436,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "snpSift_rmInfo", "ensembl_vep", - "bcftools_plugin_split_vep", - "snpSift_filter" + "snpSift_filter", + "snpSift_rmInfo", + "bcftools_plugin_split_vep" ], "update_time": "2022-10-18", "versions": 1 @@ -53248,8 +68460,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "snpSift_rmInfo", "snpSift_filter", + "snpSift_rmInfo", "snpEff" ], "update_time": "2022-10-17", @@ -53273,13 +68485,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", - "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "tp_sorted_uniq", + "datamash_ops" ], "update_time": "2022-10-15", "versions": 1 @@ -53289,19 +68501,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", + "Copy number estimation", + "Sequence alignment", "Genome alignment", - "Sequence composition calculation", "SNP annotation", - "Read mapping", "Sequencing quality control", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Copy number estimation", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "5ed38d8114bcd6f7", @@ -53316,49 +68528,49 @@ "miracum" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", + "__EXTRACT_DATASET__", "snpSift_extractFields", - "samtools_view", - "__FILTER_FROM_FILE__", + "trimmomatic", + "collapse_dataset", + "tp_find_and_replace", + "Grep1", + "bg_column_arrange_by_header", "fastqc", - "circos", - "__BUILD_LIST__", - "split_file_to_collection", - "vcfanno", + "__APPLY_RULES__", + "add_line_to_file", + "qualimap_bamqc", + "samtools_calmd", "ensembl_vep", - "__EXTRACT_DATASET__", - "tp_find_and_replace", - "tp_replace_in_line", - "__MERGE_COLLECTION__", - "datamash_ops", + "param_value_from_file", "Filter1", - "tp_text_file_with_recurring_lines", - "snpSift_filter", "Add_a_column1", + "__MERGE_COLLECTION__", + "vcf2maf", + "multiqc", + "__BUILD_LIST__", + "__SORTLIST__", + "Convert characters1", + "bcftools_plugin_split_vep", + "bwa_mem", + "tp_easyjoin_tool", "bamleftalign", - "datamash_transpose", - "collapse_dataset", - "add_line_to_file", - "param_value_from_file", + "samtools_view", "compose_text_param", - "Convert characters1", - "__SORTLIST__", + "tp_replace_in_line", + "tp_replace_in_column", "__RELABEL_FROM_FILE__", - "__APPLY_RULES__", - "qualimap_bamqc", "varscan_somatic", - "tp_replace_in_column", - "bwa_mem", - "samtools_calmd", - "trimmomatic", - "Cut1", + "datamash_ops", "samtools_rmdup", - "bcftools_plugin_split_vep", - "vcf2maf", - "multiqc", "control_freec", - "Grep1" + "datamash_transpose", + "vcfanno", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "circos", + "snpSift_filter", + "Cut1", + "__FILTER_FROM_FILE__" ], "update_time": "2022-10-15", "versions": 1 @@ -53368,17 +68580,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment analysis", + "Variant calling", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "4f62794453f65cba", @@ -53391,23 +68603,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "snpEff_databases", - "bwa_mem", - "bamleftalign", "samtools_calmd", - "trimmomatic", - "snpEff_download", - "bg_column_arrange_by_header", "varscan_somatic", - "gemini_load", "samtools_rmdup", - "gemini_query", - "gemini_annotate", "snpEff", - "multiqc", + "gemini_load", + "trimmomatic", + "snpEff_download", "fastqc", - "bamFilter" + "gemini_annotate", + "gemini_query", + "multiqc", + "tp_easyjoin_tool", + "bwa_mem", + "snpEff_databases", + "bamFilter", + "bg_column_arrange_by_header", + "bamleftalign" ], "update_time": "2022-10-14", "versions": 0 @@ -53455,12 +68667,12 @@ "proteomics" ], "tools": [ + "Paste1", "Add_a_column1", - "Grep1", - "Cut1", - "ggplot2_histogram", "histogram_rpy", - "Paste1" + "ggplot2_histogram", + "Grep1", + "Cut1" ], "update_time": "2022-10-03", "versions": 5 @@ -53470,24 +68682,24 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", + "Differential gene expression analysis", + "Primer removal", "Sequencing quality control", + "Sequence trimming", "Formatting", - "Differential gene expression analysis", - "Sequence contamination filtering", "Read pre-processing", - "Sequence trimming", - "Genome indexing", - "Nucleic acid sequence analysis", "Generation", + "Genome indexing", "Sequence composition calculation", - "Read mapping", - "Sequence alignment", "Variant calling", - "Statistical calculation", - "Primer removal", - "RNA-Seq analysis", - "Validation" + "Validation", + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "f33b5135ee99e0dc", @@ -53500,14 +68712,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", "htseq_count", "rseqc_bam2wig", "ngsutils_bam_filter", "multiqc", + "bwa_mem", "fastqc", - "deseq2", - "cutadapt" + "cutadapt", + "deseq2" ], "update_time": "2022-09-26", "versions": 8 @@ -53517,17 +68729,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Ab-initio gene prediction", - "Genome visualisation", - "Sequence assembly validation", - "Genome annotation", "Gene prediction", + "Genome annotation", "Homology-based gene prediction", - "Scaffolding", "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Operation", - "Transcriptome assembly" + "Sequence assembly validation", + "Ab-initio gene prediction", + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "26ad77bc07a7e512", @@ -53540,15 +68752,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "maker_map_ids", "jcvi_gff_stats", "gffread", - "maker", - "augustus_training", "fasta-stats", + "snap_training", "busco", + "maker_map_ids", + "maker", "jbrowse", - "snap_training" + "augustus_training" ], "update_time": "2022-09-26", "versions": 9 @@ -53558,16 +68770,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", "Peak calling", - "Gene regulatory network analysis", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation" + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "d4603d244cf8ac5b", @@ -53580,13 +68792,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", + "macs2_callpeak", + "wig_to_bigWig", "deeptools_plot_heatmap", "trim_galore", - "wig_to_bigWig", - "fastqc", "deeptools_compute_matrix", - "macs2_callpeak", - "bowtie2" + "fastqc" ], "update_time": "2022-09-23", "versions": 4 @@ -53614,13 +68826,13 @@ "convert" ], "tools": [ - "tp_easyjoin_tool", + "sort1", "table_compute", - "tp_awk_tool", - "tp_cut_tool", "tp_sed_tool", - "sort1", - "annotatemyids" + "tp_easyjoin_tool", + "tp_cut_tool", + "annotatemyids", + "tp_awk_tool" ], "update_time": "2022-09-19", "versions": 7 @@ -53645,15 +68857,15 @@ "name:scrna-seq" ], "tools": [ + "monocle3_orderCells", "monocle3_diffExp", + "monocle3_create", "monocle3_partition", + "monocle3_reduceDim", "monocle3_topmarkers", - "monocle3_learnGraph", "monocle3_plotCells", - "monocle3_orderCells", - "monocle3_preprocess", - "monocle3_create", - "monocle3_reduceDim" + "monocle3_learnGraph", + "monocle3_preprocess" ], "update_time": "2022-09-19", "versions": 3 @@ -53679,13 +68891,13 @@ "name:anndata2monocle" ], "tools": [ - "anndata_inspect", - "datamash_transpose", "regexColumn1", + "Filter1", + "datamash_transpose", + "join1", "tp_cut_tool", "Cut1", - "join1", - "Filter1" + "anndata_inspect" ], "update_time": "2022-09-19", "versions": 4 @@ -53708,12 +68920,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "__DATA_FETCH__", - "comp1", - "datamash_ops", "sort1", + "__DATA_FETCH__", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-09-18", "versions": 0 @@ -53723,9 +68935,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "ccec1752fcac5e3f", @@ -53738,8 +68950,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2022-09-12", "versions": 1 @@ -53765,24 +68977,24 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "anndata_manipulate", - "anndata_ops", - "join1", "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "anndata_manipulate", + "anndata_ops", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2022-09-05", "versions": 7 @@ -53806,14 +69018,14 @@ "name:single-cell" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", - "anndata_ops", - "Cut1", - "scanpy_read_10x", "Paste1", + "scanpy_read_10x", + "retrieve_scxa", + "anndata_ops", + "anndata_manipulate", "tp_replace_in_column", - "retrieve_scxa" + "Cut1", + "anndata_inspect" ], "update_time": "2022-09-05", "versions": 5 @@ -53837,11 +69049,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2022-08-28", "versions": 2 @@ -53853,9 +69065,9 @@ ], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "9ed36a6849fa2014", @@ -53871,15 +69083,15 @@ "name:training" ], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2022-08-27", "versions": 1 @@ -53889,11 +69101,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -53907,8 +69119,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2022-08-23", "versions": 2 @@ -53918,11 +69130,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -53936,8 +69148,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2022-08-23", "versions": 1 @@ -53947,13 +69159,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "519e0ffdfd1790bc", @@ -53966,10 +69178,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", + "cutadapt", "fastqe", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2022-08-23", "versions": 2 @@ -53990,13 +69202,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "mofa", - "rank_genes_and_peaks_muon", "cluster_mofa_embeddings_with_mudata", + "mofa", "visualise_markers_mudata", - "assign_cell_type_labels_mudata", + "rank_genes_and_peaks_muon", "mudata_import", - "compare_annotations" + "compare_annotations", + "assign_cell_type_labels_mudata" ], "update_time": "2022-08-22", "versions": 0 @@ -54019,13 +69231,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-08-21", "versions": 0 @@ -54046,9 +69258,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", - "Remove beginning1", "tp_sorted_uniq", + "Remove beginning1", + "Cut1", "csv_to_tabular" ], "update_time": "2022-08-21", @@ -54072,11 +69284,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-08-21", "versions": 0 @@ -54099,13 +69311,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-08-21", "versions": 1 @@ -54130,13 +69342,13 @@ "name" ], "tools": [ - "ggplot2_point", "Cut1", - "datamash_ops", "Remove beginning1", - "bg_uniq", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops", + "bg_uniq" ], "update_time": "2022-08-21", "versions": 1 @@ -54159,13 +69371,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", - "datamash_ops", "Remove beginning1", - "bg_uniq", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops", + "bg_uniq" ], "update_time": "2022-08-21", "versions": 3 @@ -54177,10 +69389,10 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "6dbc84168feea337", @@ -54193,10 +69405,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "__UNZIP_COLLECTION__", "multiqc", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "__UNZIP_COLLECTION__", + "fastqc" ], "update_time": "2022-08-19", "versions": 6 @@ -54219,12 +69431,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-08-18", "versions": 1 @@ -54245,19 +69457,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", "regexColumn1", + "cat1", + "sort1", + "Filter1", "wc_gnu", - "Count1", "column_remove_by_header", "Cut1", - "join1", - "tp_sorted_uniq", - "datamash_ops", - "sort1", "Remove beginning1", + "Count1", "tabular_to_csv", - "Filter1" + "join1", + "tp_sorted_uniq", + "datamash_ops" ], "update_time": "2022-08-18", "versions": 0 @@ -54280,9 +69492,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tp_head_tool", "tp_sort_header_tool", "datamash_ops", - "tp_head_tool", "bedtools_intersectbed" ], "update_time": "2022-08-10", @@ -54293,12 +69505,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3a8150c81b90a3a7", @@ -54311,23 +69523,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "gffcompare", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", - "filter_tabular", "sqlite_to_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "stringtie", + "hisat2", + "bed_to_protein_map" ], "update_time": "2022-08-08", "versions": 0 @@ -54348,9 +69560,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_split_on_column", - "Cut1", "music_compare", + "Cut1", + "tp_split_on_column", "music_construct_eset" ], "update_time": "2022-08-05", @@ -54361,13 +69573,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "6d06bd22f206e176", @@ -54388,14 +69600,14 @@ "rarefaction" ], "tools": [ - "mothur_chimera_uchime", "mothur_get_oturep", - "mothur_remove_seqs", + "muscle", + "mothur_chimera_uchime", "mothur_cluster", - "mothur_unique_seqs", - "mothur_dist_seqs", + "mothur_remove_seqs", "mothur_rarefaction_single", - "muscle" + "mothur_dist_seqs", + "mothur_unique_seqs" ], "update_time": "2022-07-29", "versions": 8 @@ -54405,10 +69617,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", + "Peptide database search", "Visualisation", - "Prediction and recognition", - "Peptide database search" + "Conversion", + "Prediction and recognition" ], "edam_topic": [], "id": "8a85663218676b59", @@ -54423,17 +69635,17 @@ "name:covid" ], "tools": [ - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", "mz_to_sqlite", - "Filter1", - "Grep1" + "Cut1", + "peptide_shaker" ], "update_time": "2022-07-15", "versions": 3 @@ -54443,12 +69655,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "RNA-Seq analysis", - "Genome indexing", "Generation", + "Genome indexing", "Sequence alignment", - "Transcriptome assembly" + "Transcriptome assembly", + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1cd85fe90839c10d", @@ -54461,11 +69673,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", "bowtie2", "bwa", - "hisat2", - "stringtie" + "bwa_mem", + "stringtie", + "hisat2" ], "update_time": "2022-07-13", "versions": 0 @@ -54475,15 +69687,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", + "Statistical calculation", + "Gene expression analysis", "Sequencing quality control", "Formatting", - "Gene expression analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Pathway or network analysis", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "65aed668233d5f73", @@ -54496,11 +69708,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tximport", "trimmomatic", "salmon", "fasterq_dump", - "fastqc" + "fastqc", + "tximport" ], "update_time": "2022-07-12", "versions": 1 @@ -54521,15 +69733,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "collapse_dataset", - "Cut1", "tab2fasta", "ncbi_blastp_wrapper", + "tp_cat", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "tp_cat" + "query_tabular", + "Cut1" ], "update_time": "2022-07-03", "versions": 1 @@ -54539,18 +69751,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Conversion", - "Clustering", - "Heat map generation", - "Protein quantification", - "Formatting", - "Imputation", - "Standardisation and normalisation", "Visualisation", "Statistical calculation", + "Formatting", + "Clustering", + "Standardisation and normalisation", + "Principal component plotting", + "Conversion", + "Protein quantification", "Peptide database search", - "Principal component plotting" + "Imputation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "eb54512829d8509c", @@ -54564,22 +69776,22 @@ "tags": [], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "mz_to_sqlite", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", - "tp_cat", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "mz_to_sqlite", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2022-07-03", "versions": 1 @@ -54600,15 +69812,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "collapse_dataset", - "Cut1", "tab2fasta", "ncbi_blastp_wrapper", + "tp_cat", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "tp_cat" + "query_tabular", + "Cut1" ], "update_time": "2022-07-03", "versions": 6 @@ -54618,18 +69830,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Conversion", - "Clustering", - "Heat map generation", - "Protein quantification", - "Formatting", - "Imputation", - "Standardisation and normalisation", "Visualisation", "Statistical calculation", + "Formatting", + "Clustering", + "Standardisation and normalisation", + "Principal component plotting", + "Conversion", + "Protein quantification", "Peptide database search", - "Principal component plotting" + "Imputation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "41e9882300fa2386", @@ -54643,22 +69855,22 @@ "tags": [], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "mz_to_sqlite", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", - "tp_cat", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "mz_to_sqlite", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2022-07-03", "versions": 10 @@ -54680,10 +69892,10 @@ "tags": [], "tools": [ "collapse_dataset", - "Cut1", "Remove beginning1", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2022-06-29", "versions": 4 @@ -54705,10 +69917,10 @@ "tags": [], "tools": [ "collapse_dataset", - "Cut1", "Remove beginning1", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2022-06-29", "versions": 3 @@ -54730,10 +69942,10 @@ "tags": [], "tools": [ "collapse_dataset", - "Cut1", "Remove beginning1", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2022-06-29", "versions": 3 @@ -54754,11 +69966,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "collapse_dataset", - "Cut1", "pepquery", "Grouping1", - "Filter1" + "Cut1" ], "update_time": "2022-06-29", "versions": 1 @@ -54768,18 +69980,18 @@ "creators": [], "doi": "", "edam_operation": [ + "Copy number estimation", + "Statistical calculation", "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", "Sequence alignment", - "Variant calling", - "Statistical calculation", - "Copy number estimation", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "b1d1694b95ed10e1", @@ -54794,21 +70006,21 @@ "miracum" ], "tools": [ - "fastqc", - "bwa_mem", - "bamleftalign", "samtools_calmd", - "trimmomatic", - "circos", - "samtools_view", "samtools_rmdup", + "control_freec", + "trimmomatic", + "multiqc", "tp_replace_in_line", + "__BUILD_LIST__", + "Grep1", "tp_text_file_with_recurring_lines", + "fastqc", + "bwa_mem", + "circos", + "bamleftalign", "__RELABEL_FROM_FILE__", - "multiqc", - "control_freec", - "__BUILD_LIST__", - "Grep1" + "samtools_view" ], "update_time": "2022-06-28", "versions": 0 @@ -54829,13 +70041,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", "collapse_dataset", - "Cut1", - "pepquery", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", - "Filter1" + "query_tabular", + "Cut1" ], "update_time": "2022-06-24", "versions": 11 @@ -54859,8 +70071,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2022-06-16", "versions": 1 @@ -54870,17 +70082,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", + "Sequence alignment analysis", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "99022559adf01c4a", @@ -54893,17 +70105,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", + "freebayes", + "snpEff", + "samtools_idxstats", + "fastqc", "pileup_parser", - "bwa_mem", - "samtools_flagstat", - "sam_pileup", "bamtools", - "snpEff", - "freebayes", "picard_SortSam", - "fastqc", - "Filter1", - "samtools_idxstats" + "bwa_mem", + "sam_pileup", + "samtools_flagstat" ], "update_time": "2022-06-13", "versions": 0 @@ -54913,17 +70125,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", + "Sequence alignment analysis", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "36a4646959829018", @@ -54936,17 +70148,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Filter1", + "freebayes", + "snpEff", + "samtools_idxstats", + "fastqc", "pileup_parser", - "bwa_mem", - "samtools_flagstat", - "sam_pileup", "bamtools", - "snpEff", - "freebayes", "picard_SortSam", - "fastqc", - "Filter1", - "samtools_idxstats" + "bwa_mem", + "sam_pileup", + "samtools_flagstat" ], "update_time": "2022-06-13", "versions": 0 @@ -54956,20 +70168,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence composition calculation", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Statistical calculation" + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ad4b347f9b68e127", @@ -54984,20 +70196,20 @@ "cut_and_run" ], "tools": [ - "bamFilter", - "Extract genomic DNA 1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", + "macs2_callpeak", + "pe_histogram", + "meme_chip", + "bedtools_intersectbed", "trim_galore", + "Extract genomic DNA 1", "macs2_predictd", - "meme_chip", - "__APPLY_RULES__", - "fastqc", - "macs2_callpeak", + "bedtools_bamtobed", "__FLATTEN__", - "bedtools_intersectbed", - "pe_histogram" + "fastqc", + "bamFilter", + "__APPLY_RULES__", + "picard_MarkDuplicates" ], "update_time": "2022-06-13", "versions": 30 @@ -55021,16 +70233,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "circos_interval_to_text", "Add_a_column1", - "circos_interval_to_tile", "Cut1", - "tp_grep_tool", + "circos_interval_to_text", + "tp_cat", "mitos2", - "circos", "tp_replace_in_column", - "fasta_compute_length", - "tp_cat" + "circos", + "circos_interval_to_tile", + "tp_grep_tool", + "fasta_compute_length" ], "update_time": "2022-06-10", "versions": 0 @@ -55040,10 +70252,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Alignment", "Genome annotation", + "Validation", "Visualisation", - "Validation" + "Alignment" ], "edam_topic": [], "id": "0a692a2e643b9e1a", @@ -55079,19 +70291,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "scanpy_compute_graph", "scanpy_plot_embed", - "scanpy_run_tsne", "scanpy_run_umap", "scanpy_run_pca", - "scanpy_find_variable_genes", - "scanpy_normalise_data", + "scanpy_filter_genes", "scanpy_remove_confounders", - "scanpy_find_cluster", "scanpy_scale_data", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2022-06-10", "versions": 20 @@ -55112,11 +70324,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "xarray_metadata_info", - "graphicsmagick_image_montage", "xarray_coords_info", + "cdo_operations", + "graphicsmagick_image_montage", "xarray_mapplot", - "cdo_operations" + "xarray_metadata_info" ], "update_time": "2022-06-07", "versions": 2 @@ -55142,10 +70354,10 @@ "climate" ], "tools": [ - "xarray_metadata_info", "xarray_coords_info", - "xarray_mapplot", - "cdo_operations" + "xarray_metadata_info", + "cdo_operations", + "xarray_mapplot" ], "update_time": "2022-06-07", "versions": 3 @@ -55172,12 +70384,12 @@ "3.24" ], "tools": [ + "fastq_combiner", + "fastq_to_fasta_python", + "collapse_dataset", "bg_sortmerna", "fasplit", - "collapse_dataset", - "fastq_paired_end_interlacer", - "fastq_combiner", - "fastq_to_fasta_python" + "fastq_paired_end_interlacer" ], "update_time": "2022-06-06", "versions": 3 @@ -55187,14 +70399,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Phylogenetic tree analysis", "Visualisation", + "Nucleic acid sequence analysis", + "Phylogenetic tree editing", + "Phylogenetic tree analysis", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Nucleic acid sequence analysis", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "4f21205e71cabd37", @@ -55207,12 +70419,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metaphlan", + "export2graphlan", "graphlan_annotate", - "Cut1", - "graphlan", "taxonomy_krona_chart", - "export2graphlan" + "graphlan", + "metaphlan", + "Cut1" ], "update_time": "2022-06-06", "versions": 3 @@ -55222,13 +70434,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "3183c2abca463bb4", @@ -55241,9 +70453,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2022-06-06", "versions": 4 @@ -55253,14 +70465,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Data handling", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "7783eeebfa264bf5", @@ -55274,20 +70486,20 @@ "tags": [], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", + "mothur_classify_otu", + "mothur_make_group", "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", + "mothur_pre_cluster", + "mothur_summary_seqs", + "mothur_align_seqs", "fasterq_dump", - "mothur_unique_seqs", "mothur_filter_seqs", - "mothur_make_group", - "mothur_classify_otu", - "mothur_summary_seqs", - "mothur_merge_files", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2022-05-29", "versions": 7 @@ -55297,14 +70509,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Data handling", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "6efd80daabf518bf", @@ -55318,18 +70530,18 @@ "tags": [], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", + "mothur_classify_otu", "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", + "mothur_pre_cluster", + "mothur_summary_seqs", + "mothur_align_seqs", "fasterq_dump", "mothur_filter_seqs", - "mothur_classify_otu", - "mothur_summary_seqs", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs" ], "update_time": "2022-05-29", "versions": 1 @@ -55340,10 +70552,10 @@ "doi": "", "edam_operation": [ "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic tree analysis", "Nucleic acid sequence analysis", - "Phylogenetic analysis" + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Taxonomic classification" ], "edam_topic": [], "id": "21a17d6c473a88c0", @@ -55356,14 +70568,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "humann_regroup_table", + "humann_rename_table", "combine_metaphlan2_humann2", - "Cut1", + "merge_metaphlan_tables", "Grep1", - "humann_regroup_table", - "humann_join_tables", "humann_unpack_pathways", - "merge_metaphlan_tables", - "humann_rename_table" + "humann_join_tables", + "Cut1" ], "update_time": "2022-05-24", "versions": 5 @@ -55373,11 +70585,11 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree editing", "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "b5f848dc8e96663c", @@ -55390,12 +70602,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metaphlan2krona", + "export2graphlan", "graphlan_annotate", - "Cut1", "graphlan", "krona-text", - "export2graphlan" + "metaphlan2krona", + "Cut1" ], "update_time": "2022-05-24", "versions": 4 @@ -55406,8 +70618,8 @@ "doi": "", "edam_operation": [ "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" + "Phylogenetic analysis", + "Taxonomic classification" ], "edam_topic": [], "id": "3118d383c81cf805", @@ -55420,15 +70632,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "combine_metaphlan2_humann2", - "Cut1", - "humann_renorm_table", - "humann", "humann_regroup_table", + "humann_rename_table", + "humann", + "combine_metaphlan2_humann2", + "Grep1", "humann_unpack_pathways", "humann_split_stratified_table", - "Grep1", - "humann_rename_table" + "Cut1", + "humann_renorm_table" ], "update_time": "2022-05-24", "versions": 1 @@ -55438,26 +70650,26 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Phylogenetic tree analysis", - "Sequencing quality control", - "Phylogenetic analysis", - "Sequence comparison", "Visualisation", + "Primer removal", + "Sequencing quality control", + "Phylogenetic tree analysis", + "Sequence similarity search", + "Species frequency estimation", + "Conversion", "Phylogenetic inference", - "Read pre-processing", "Sequence trimming", - "Phylogenetic tree visualisation", + "Statistical calculation", "Nucleic acid sequence analysis", + "Sequence comparison", + "Phylogenetic analysis", "Phylogenetic tree editing", - "Species frequency estimation", "Sequence composition calculation", - "Statistical calculation", - "Primer removal", - "Taxonomic classification", - "Validation" + "Read pre-processing", + "Sequence alignment analysis", + "Validation", + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "4d32b1b3ac0a7161", @@ -55472,29 +70684,29 @@ "xy" ], "tools": [ - "combine_metaphlan2_humann2", - "graphlan", + "fastq_combiner", + "collapse_dataset", "humann", + "combine_metaphlan2_humann2", + "Grep1", "fastq_paired_end_interlacer", - "taxonomy_krona_chart", + "humann_unpack_pathways", "fastqc", - "fastq_to_fasta_python", - "humann_rename_table", "metaphlan", - "fasplit", - "graphlan_annotate", - "bg_sortmerna", - "collapse_dataset", - "humann_renorm_table", - "fastq_combiner", - "export2graphlan", - "Cut1", - "humann_regroup_table", - "humann_unpack_pathways", "humann_split_stratified_table", + "humann_regroup_table", + "humann_rename_table", + "fastq_to_fasta_python", "multiqc", - "Grep1", - "cutadapt" + "cutadapt", + "export2graphlan", + "bg_sortmerna", + "taxonomy_krona_chart", + "graphlan_annotate", + "fasplit", + "graphlan", + "Cut1", + "humann_renorm_table" ], "update_time": "2022-05-24", "versions": 1 @@ -55504,15 +70716,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Species frequency estimation", - "Phylogenetic tree analysis", + "Nucleic acid sequence analysis", + "Phylogenetic tree editing", "Phylogenetic analysis", + "Phylogenetic tree analysis", + "Species frequency estimation", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Nucleic acid sequence analysis", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "713a5485e2007f90", @@ -55525,19 +70737,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metaphlan2krona", + "humann_regroup_table", + "humann_rename_table", + "export2graphlan", "graphlan_annotate", "combine_metaphlan2_humann2", - "Cut1", - "export2graphlan", + "merge_metaphlan_tables", "Grep1", - "graphlan", - "humann_regroup_table", - "humann_join_tables", "humann_unpack_pathways", - "merge_metaphlan_tables", + "graphlan", + "metaphlan2krona", "krona-text", - "humann_rename_table" + "humann_join_tables", + "Cut1" ], "update_time": "2022-05-24", "versions": 2 @@ -55547,9 +70759,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "da3a6d229e422dde", @@ -55562,8 +70774,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2022-05-18", "versions": 1 @@ -55584,16 +70796,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seurat_find_variable_genes", "seurat_scale_data", "seurat_find_neighbours", - "seurat_run_tsne", - "seurat_normalise_data", - "seurat_find_markers", - "sceasy_convert", "seurat_run_pca", "seurat_find_clusters", + "seurat_normalise_data", + "sceasy_convert", + "seurat_find_markers", "seurat_filter_cells", + "seurat_run_tsne", + "seurat_find_variable_genes", "seurat_dim_plot" ], "update_time": "2022-05-16", @@ -55604,14 +70816,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Loading", - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Community profiling", + "Loading", + "Data handling" ], "edam_topic": [], "id": "af7c349497a75314", @@ -55624,13 +70836,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "dropletutils", - "rna_star", - "featurecounts", "umi_tools_count", - "__UNZIP_COLLECTION__", + "featurecounts", + "dropletutils", + "bamFilter", "umi_tools_extract", - "bamFilter" + "rna_star", + "__UNZIP_COLLECTION__" ], "update_time": "2022-05-16", "versions": 3 @@ -55666,11 +70878,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Loading", "Sequence composition calculation", - "Community profiling", "Gene expression analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Loading", + "Community profiling" ], "edam_topic": [], "id": "83ae28e23099a3f6", @@ -55683,10 +70895,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "_ensembl_gtf2gene_list", "__UNZIP_COLLECTION__", - "alevin", + "_ensembl_gtf2gene_list", "_salmon_kallisto_mtx_to_10x", + "alevin", "dropletutils" ], "update_time": "2022-05-16", @@ -55714,20 +70926,20 @@ "iwc" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-05-13", "versions": 2 @@ -55748,12 +70960,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "xarray_metadata_info", - "graphicsmagick_image_montage", "xarray_coords_info", - "xarray_mapplot", "cdo_operations", - "xarray_netcdf2netcdf" + "graphicsmagick_image_montage", + "xarray_netcdf2netcdf", + "xarray_mapplot", + "xarray_metadata_info" ], "update_time": "2022-05-03", "versions": 0 @@ -55774,28 +70986,28 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_ops", - "bg_column_arrange_by_header", - "scanpy_read_10x", - "__BUILD_LIST__", + "scanpy_find_markers", "scanpy_filter_genes", - "scanpy_run_umap", - "scanpy_parameter_iterator", - "__MERGE_COLLECTION__", - "tp_replace_in_line", - "scanpy_integrate_harmony", - "scanpy_find_variable_genes", - "__FILTER_FAILED_DATASETS__", + "bg_column_arrange_by_header", "join1", + "scanpy_normalise_data", "scanpy_compute_graph", + "scanpy_integrate_harmony", + "__MERGE_COLLECTION__", + "__BUILD_LIST__", + "scanpy_find_variable_genes", + "scanpy_filter_cells", + "scanpy_run_umap", "scanpy_run_tsne", - "scanpy_find_markers", - "scanpy_find_cluster", + "tp_replace_in_line", "scanpy_run_pca", - "Cut1", + "scanpy_find_cluster", + "scanpy_read_10x", + "anndata_ops", + "scanpy_parameter_iterator", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "scanpy_normalise_data", - "scanpy_filter_cells" + "Cut1" ], "update_time": "2022-04-27", "versions": 2 @@ -55823,9 +71035,9 @@ "mitochondrion_tracking" ], "tools": [ - "ip_curve_fitting", "ip_spot_detection_2d", - "ip_points_association_nn" + "ip_points_association_nn", + "ip_curve_fitting" ], "update_time": "2022-04-25", "versions": 21 @@ -55846,13 +71058,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "xarray_metadata_info", - "graphicsmagick_image_montage", "xarray_coords_info", - "xarray_mapplot", "cdo_operations", + "graphicsmagick_image_montage", "xarray_netcdf2netcdf", - "xarray_select" + "xarray_select", + "xarray_mapplot", + "xarray_metadata_info" ], "update_time": "2022-04-20", "versions": 4 @@ -55862,13 +71074,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Differential gene expression analysis", + "RNA-Seq analysis", "Sequence alignment", + "Differential gene expression analysis", + "RNA-Seq quantification", "Read summarisation", - "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence annotation", + "Transcriptome assembly" ], "edam_topic": [], "id": "e8202b7b6338005d", @@ -55881,12 +71093,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gffcompare", - "stringtie_merge", "featurecounts", + "stringtie_merge", + "gffcompare", + "stringtie", "hisat2", - "deseq2", - "stringtie" + "deseq2" ], "update_time": "2022-04-13", "versions": 3 @@ -55898,8 +71110,8 @@ ], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "6e5f0d05c91876c2", @@ -55912,20 +71124,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", + "filter_tabular", + "Filter1", + "mz_to_sqlite", + "query_tabular", "collapse_dataset", "Cut1", + "fasta2tab", + "Grep1", + "search_gui", "pepquery", - "query_tabular", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "mz_to_sqlite", - "filter_tabular", - "Filter1", - "Grep1" + "peptide_shaker" ], "update_time": "2022-04-11", "versions": 1 @@ -55937,8 +71149,8 @@ ], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "03e52c8c71710cae", @@ -55954,19 +71166,19 @@ "name:oldsgps" ], "tools": [ - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", + "filter_tabular", + "Filter1", + "mz_to_sqlite", + "query_tabular", "collapse_dataset", "Cut1", + "fasta2tab", + "search_gui", "pepquery", - "query_tabular", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "mz_to_sqlite", - "filter_tabular", - "Filter1" + "peptide_shaker" ], "update_time": "2022-04-11", "versions": 2 @@ -55978,8 +71190,8 @@ ], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "9a8b5e99ca9500e3", @@ -55994,20 +71206,20 @@ "name:covid19" ], "tools": [ - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", + "filter_tabular", + "Filter1", + "mz_to_sqlite", + "query_tabular", "collapse_dataset", "Cut1", + "fasta2tab", + "search_gui", "ident_params", "pepquery", - "query_tabular", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "mz_to_sqlite", - "filter_tabular", - "Filter1" + "peptide_shaker" ], "update_time": "2022-04-11", "versions": 1 @@ -56017,17 +71229,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "5a16af00bf8bf57b", @@ -56040,16 +71252,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "picard_MarkDuplicates", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "Cut1", - "freebayes", + "vcf2tsv", + "bwa_mem", "fastqc", "bamFilter", - "vcf2tsv" + "Cut1", + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2022-04-10", "versions": 0 @@ -56072,13 +71284,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-04-08", "versions": 0 @@ -56099,8 +71311,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cardinal_preprocessing", "cardinal_filtering", + "cardinal_preprocessing", "cardinal_data_exporter" ], "update_time": "2022-04-08", @@ -56112,9 +71324,9 @@ "doi": "", "edam_operation": [ "Read mapping", + "Phylogenetic tree generation", "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Variant calling" ], "edam_topic": [], "id": "464b642261ed7452", @@ -56149,11 +71361,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sort1", "Add_a_column1", + "gops_join_1", "tp_sort_header_tool", - "sort1", - "Grouping1", - "gops_join_1" + "Grouping1" ], "update_time": "2022-03-31", "versions": 1 @@ -56177,12 +71389,12 @@ ], "tools": [ "FileConverter", + "PeakPickerHiRes", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", "ident_params", - "Grep1", - "PeakPickerHiRes" + "fasta_cli", + "peptide_shaker" ], "update_time": "2022-03-31", "versions": 6 @@ -56192,15 +71404,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", "Visualisation", "Statistical calculation", - "RNA-Seq analysis", + "Differential gene expression analysis", + "Sequence alignment", + "Sequencing quality control", + "Transcriptome assembly", + "Sequence composition calculation", "Validation", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "82ef590b5821805d", @@ -56213,29 +71425,29 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_multijoin_tool", - "volcanoplot", + "trimmomatic", "table_compute", + "tp_cat", + "join1", "fastqc", + "ggplot2_point", + "Filter1", + "Add_a_column1", "sort1", - "hisat2", + "multiqc", + "tp_multijoin_tool", + "stringtie", + "addValue", "deseq2", - "Add_a_column1", + "cat1", "subtract_query1", "ggplot2_pca", - "join1", - "addValue", - "stringtie", "tp_replace_in_column", - "cat1", - "ggplot2_heatmap2", - "trimmomatic", - "ggplot2_point", - "Cut1", + "hisat2", + "volcanoplot", "Remove beginning1", - "multiqc", - "Filter1", - "tp_cat" + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2022-03-28", "versions": 3 @@ -56245,16 +71457,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Differential gene expression analysis", - "Genome assembly", - "Sequence assembly validation", "Gene prediction", - "Antimicrobial resistance prediction", - "Scaffolding", "Genome annotation", "Sequence clustering", + "Genome assembly", + "Differential gene expression analysis", + "Scaffolding", + "Transcriptome assembly", "Coding region prediction", - "Transcriptome assembly" + "Sequence assembly validation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "6984990d0ac2e1e6", @@ -56267,10 +71479,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "prokka", "antismash", "abricate", - "busco", - "prokka" + "busco" ], "update_time": "2022-03-28", "versions": 5 @@ -56280,18 +71492,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Genome assembly", "Scatter plot plotting", - "Base-calling", - "De-novo assembly", + "Sequence assembly visualisation", + "Mapping assembly", "Sequence assembly", "Sequencing quality control", - "Variant calling", + "Base-calling", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Cross-assembly", + "De-novo assembly", + "Variant calling", + "Filtering" ], "edam_topic": [], "id": "86cf02cc0868d238", @@ -56305,12 +71517,12 @@ "tags": [], "tools": [ "flye", + "bandage_info", + "nanoplot", "porechop", "filtlong", "bandage_image", - "nanoplot", - "medaka_consensus_pipeline", - "bandage_info" + "medaka_consensus_pipeline" ], "update_time": "2022-03-28", "versions": 3 @@ -56320,10 +71532,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", "Visualisation", "Box-Whisker plot plotting", - "Scatter plot plotting" + "Scatter plot plotting", + "Taxonomic classification" ], "edam_topic": [], "id": "0bafeb17c21ebc9c", @@ -56336,10 +71548,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "taxonomy_krona_chart", "nanoplot", - "Kraken2Tax", - "kraken2" + "taxonomy_krona_chart", + "kraken2", + "Kraken2Tax" ], "update_time": "2022-03-27", "versions": 2 @@ -56349,29 +71561,29 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence similarity search", + "Genome annotation", "Sequence assembly", + "Mapping assembly", + "Scaffolding", "Sequencing quality control", - "Differential gene expression analysis", + "Base-calling", + "Cross-assembly", + "Sequence similarity search", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Scaffolding", + "Coding region prediction", + "Transcriptome assembly", + "Sequence assembly validation", "Genome alignment", + "Gene prediction", "Sequence clustering", "Genome assembly", - "Mapping assembly", - "Transcriptome assembly", - "Cross-assembly", - "Filtering", + "Differential gene expression analysis", "Scatter plot plotting", + "Sequence assembly visualisation", + "De-novo assembly", "Variant calling", - "Sequence assembly validation", - "Gene prediction", - "Genome annotation", - "Coding region prediction", - "Base-calling" + "Filtering", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "bf48b0eb15e8ff75", @@ -56384,17 +71596,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "abricate", - "porechop", + "prokka", "flye", - "filtlong", - "bandage_image", - "nanoplot", "fastani", - "medaka_consensus_pipeline", "antismash", + "abricate", + "nanoplot", + "porechop", + "bandage_image", "busco", - "prokka" + "medaka_consensus_pipeline", + "filtlong" ], "update_time": "2022-03-25", "versions": 8 @@ -56407,8 +71619,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Variant calling" ], "edam_topic": [], "id": "a183da6b56cd1d60", @@ -56421,8 +71633,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tb_variant_filter", - "snippy" + "snippy", + "tb_variant_filter" ], "update_time": "2022-03-21", "versions": 4 @@ -56432,18 +71644,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", "Copy number estimation", + "Sequence alignment", + "Genome alignment", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "6ed1016dfdf9f928", @@ -56458,47 +71670,47 @@ "miracum" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "gemini_load", - "samtools_view", - "__FILTER_FROM_FILE__", - "fastqc", - "circos", - "__BUILD_LIST__", - "split_file_to_collection", "__EXTRACT_DATASET__", + "trimmomatic", + "collapse_dataset", "tp_find_and_replace", - "tp_replace_in_line", - "gemini_annotate", - "__MERGE_COLLECTION__", - "datamash_ops", + "Grep1", + "bg_column_arrange_by_header", + "fastqc", + "__APPLY_RULES__", + "add_line_to_file", + "qualimap_bamqc", + "samtools_calmd", + "param_value_from_file", "Filter1", - "tp_text_file_with_recurring_lines", "Add_a_column1", - "bamleftalign", - "datamash_transpose", - "collapse_dataset", + "__MERGE_COLLECTION__", + "multiqc", + "__BUILD_LIST__", + "__SORTLIST__", + "Convert characters1", + "tp_easyjoin_tool", + "bwa_mem", "gemini_query", - "add_line_to_file", - "param_value_from_file", + "samtools_view", + "bamleftalign", "snpEff", "compose_text_param", - "Convert characters1", - "__SORTLIST__", + "gemini_annotate", + "tp_replace_in_line", + "tp_replace_in_column", "__RELABEL_FROM_FILE__", - "__APPLY_RULES__", - "qualimap_bamqc", "varscan_somatic", - "tp_replace_in_column", - "bwa_mem", - "samtools_calmd", - "trimmomatic", - "Cut1", + "datamash_ops", "samtools_rmdup", - "multiqc", "control_freec", - "Grep1" + "gemini_load", + "datamash_transpose", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "circos", + "Cut1", + "__FILTER_FROM_FILE__" ], "update_time": "2022-03-18", "versions": 4 @@ -56521,21 +71733,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2022-03-18", "versions": 1 @@ -56558,21 +71770,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2022-03-18", "versions": 1 @@ -56595,19 +71807,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2022-03-18", "versions": 1 @@ -56619,18 +71831,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "4c75ab0be3c56494", @@ -56647,21 +71859,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -56673,18 +71885,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "9feebfc6c34da287", @@ -56701,21 +71913,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -56727,18 +71939,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "74f19aff1b9cdd6b", @@ -56755,21 +71967,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -56792,15 +72004,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2022-03-18", "versions": 1 @@ -56823,15 +72035,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2022-03-18", "versions": 1 @@ -56857,20 +72069,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -56896,20 +72108,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -56935,20 +72147,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -56974,20 +72186,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -57013,20 +72225,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -57054,8 +72266,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -57083,8 +72295,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -57112,8 +72324,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -57126,11 +72338,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "f54b4d76f7f9a589", @@ -57146,15 +72358,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57167,11 +72379,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "03d1d2e0dc6e2024", @@ -57187,15 +72399,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57207,15 +72419,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "c2af7a5dbfb5b023", @@ -57231,17 +72443,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57253,15 +72465,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "07b74e4cf53cb633", @@ -57279,17 +72491,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57301,15 +72513,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "81122d30c64a52a6", @@ -57327,17 +72539,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57349,15 +72561,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "7b7ef222ac4f9887", @@ -57375,17 +72587,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -57397,14 +72609,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "6dbac47941a804da", @@ -57421,22 +72633,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57448,14 +72660,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "2573209308aaad23", @@ -57472,22 +72684,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57499,14 +72711,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "fc216dfb0ec9ed41", @@ -57523,22 +72735,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57550,14 +72762,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "0be293debca8fb9b", @@ -57574,22 +72786,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57601,14 +72813,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "ed20bd120064bab0", @@ -57625,22 +72837,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57652,14 +72864,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "a6f4371ef9bc1aab", @@ -57676,22 +72888,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57703,14 +72915,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "ee6dc47660540ba6", @@ -57727,26 +72939,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2022-03-18", "versions": 1 @@ -57758,15 +72970,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "b97532c398b821a2", @@ -57784,20 +72996,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57809,15 +73021,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "7bdd9ad918edab0b", @@ -57835,20 +73047,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57860,15 +73072,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "0f6a7bd5362e4a2b", @@ -57886,20 +73098,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -57911,16 +73123,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "2d9d4445a1871230", @@ -57938,27 +73150,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -57970,16 +73182,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "4d97068a725c975c", @@ -57997,27 +73209,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -58045,18 +73257,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -58084,18 +73296,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -58123,18 +73335,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -58162,18 +73374,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -58183,10 +73395,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Data handling", + "Sequencing quality control" ], "edam_topic": [], "id": "872f5bc9fdbbc619", @@ -58211,12 +73423,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "48071c1720b2fd8d", @@ -58229,10 +73441,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "multiqc", "rna_star", - "fasterq_dump" + "multiqc", + "fasterq_dump", + "fastqc" ], "update_time": "2022-03-11", "versions": 2 @@ -58243,8 +73455,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Variant calling" ], "edam_topic": [], "id": "65249196143d7930", @@ -58257,9 +73469,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "__MERGE_COLLECTION__", - "tb_variant_filter", "snippy", + "tb_variant_filter", + "__MERGE_COLLECTION__", "trimmomatic" ], "update_time": "2022-03-10", @@ -58283,8 +73495,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ip_landmark_registration", - "ip_projective_transformation" + "ip_projective_transformation", + "ip_landmark_registration" ], "update_time": "2022-03-07", "versions": 19 @@ -58294,22 +73506,22 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence trimming", - "Sequence assembly validation", - "Visualisation", - "Scaffolding", "Gene prediction", "Genome annotation", - "Genome assembly", + "Visualisation", "Statistical calculation", - "Coding region prediction", + "Genome assembly", "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Aggregation", + "Transcriptome assembly", + "Coding region prediction", + "Sequence composition calculation", "Read pre-processing", - "Transcriptome assembly" + "Sequence trimming", + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "165089132248a0b0", @@ -58322,12 +73534,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "prokka", + "unicycler", "trimmomatic", - "quast", "fasterq_dump", - "unicycler", + "quast", "busco", - "prokka", "fastqc", "cutadapt" ], @@ -58339,9 +73551,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", + "Annotation", "Differential gene expression analysis", - "Annotation" + "RNA-Seq analysis" ], "edam_topic": [], "id": "ca286c2fdc71e960", @@ -58355,19 +73567,19 @@ "tags": [], "tools": [ "cat1", + "Filter1", "ggplot2_heatmap2", + "venn_list", "table_compute", + "tp_cat", "tp_sort_header_tool", + "comp1", "join1", + "tp_replace_in_column", + "annotatemyids", "Cut1", - "comp1", - "Filter1", "bg_uniq", - "annotatemyids", - "deseq2", - "venn_list", - "tp_replace_in_column", - "tp_cat" + "deseq2" ], "update_time": "2022-02-28", "versions": 0 @@ -58379,14 +73591,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "579dd1e95e76402f", @@ -58404,26 +73616,26 @@ "iwc" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2022-02-28", "versions": 1 @@ -58433,8 +73645,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "e132370adf8f2838", @@ -58447,14 +73659,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", "dada2_learnErrors", - "dada2_dada", - "dada2_removeBimeraDenovo" + "dada2_mergePairs" ], "update_time": "2022-02-24", "versions": 5 @@ -58475,8 +73687,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "tp_cat" ], "update_time": "2022-02-24", @@ -58522,10 +73734,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Cut1", "pepquery", - "Filter1", "Grouping1", - "Cut1" + "Filter1" ], "update_time": "2022-02-22", "versions": 2 @@ -58535,13 +73747,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "535f777e5e42e98c", @@ -58556,9 +73768,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2022-02-21", "versions": 0 @@ -58583,9 +73795,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2022-02-21", "versions": 0 @@ -58606,9 +73818,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastq_to_fasta_python", + "fastq_stats", "cshl_fastx_reverse_complement", - "fastq_stats" + "fastq_to_fasta_python" ], "update_time": "2022-02-11", "versions": 1 @@ -58635,12 +73847,12 @@ "computational-chemistry" ], "tools": [ + "sort1", "rdconf", - "openbabel_addh", "ctb_alignit", - "sort1", + "tp_cat", "split_file_to_collection", - "tp_cat" + "openbabel_addh" ], "update_time": "2022-02-07", "versions": 52 @@ -58650,9 +73862,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d5780c37232e3181", @@ -58696,18 +73908,18 @@ "iwc" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-02-07", "versions": 1 @@ -58730,11 +73942,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-02-05", "versions": 0 @@ -58767,13 +73979,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "9e31c51911987687", @@ -58788,9 +74000,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2022-02-05", "versions": 0 @@ -58815,8 +74027,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "fastqe" + "fastqe", + "fastqc" ], "update_time": "2022-02-05", "versions": 0 @@ -58839,14 +74051,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tb_profiler_profile", - "samtools_view", - "tp_grep_tool", - "tp_sed_tool", + "addName", "__MERGE_COLLECTION__", "tp_replace_in_line", - "addName", - "tp_cat" + "tp_cat", + "tp_sed_tool", + "tp_grep_tool", + "samtools_view", + "tb_profiler_profile" ], "update_time": "2022-02-04", "versions": 10 @@ -58856,13 +74068,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "927d24dcde139b9c", @@ -58877,9 +74089,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2022-02-04", "versions": 0 @@ -58889,10 +74101,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "91d4aabba7ad40c8", @@ -58997,14 +74209,14 @@ "tags": [], "tools": [ "bcftools_consensus", - "tp_awk_tool", + "addName", + "snp_sites", "melt", + "tp_cat", + "cshl_fasta_formatter", "tb_variant_filter", - "addName", "snp_dists", - "cshl_fasta_formatter", - "snp_sites", - "tp_cat" + "tp_awk_tool" ], "update_time": "2022-02-04", "versions": 11 @@ -59014,14 +74226,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Pairwise sequence alignment", - "Variant calling", - "Formatting", "Statistical calculation", "Copy number estimation", "Genome alignment", + "Sequencing quality control", + "Formatting", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Variant calling", "Validation" ], "edam_topic": [], @@ -59035,26 +74247,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", "snpSift_extractFields", - "minimap2", - "picard_MeanQualityByCycle", "samtools_merge", + "picard_CollectWgsMetrics", "fastqc", - "picard_FixMateInformation", - "picard_artifact_metrics", - "picard_EstimateLibraryComplexity", - "freebayes", + "multiqc", "picard_CASM", "bamleftalign", - "picard_CollectWgsMetrics", - "snpEff", - "control_freec", + "picard_CollectGcBiasMetrics", "picard_MarkDuplicates", "picard_QualityScoreDistribution", + "snpEff", + "minimap2", + "picard_FixMateInformation", "picard_CollectBaseDistributionByCycle", - "multiqc", - "picard_CollectGcBiasMetrics" + "picard_CollectInsertSizeMetrics", + "freebayes", + "control_freec", + "picard_artifact_metrics", + "picard_MeanQualityByCycle", + "picard_EstimateLibraryComplexity" ], "update_time": "2022-02-03", "versions": 35 @@ -59064,16 +74276,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", + "Sequence clustering", "Genome assembly", - "Formatting", "Sequence alignment", - "Statistical calculation", - "Sequence clustering" + "Sequencing quality control", + "Sequence annotation", + "Formatting", + "Sequence composition calculation", + "Sequence alignment analysis", + "Data handling" ], "edam_topic": [], "id": "bebcbd6f0ffa55c5", @@ -59086,27 +74298,27 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seq_filter_by_id", + "samtool_filter2", + "trimmomatic", + "ncbi_blastn_wrapper", + "fasta2tab", + "bg_diamond", + "fastqc", "tp_grep_tool", + "fasterq_dump", + "fasta_merge_files_and_filter_unique_sequences", + "seq_filter_by_id", "cd_hit", - "bg_diamond", - "megahit", + "subtract_query1", "picard_SamToFastq", - "fastqc", + "megahit", + "blastxml_to_top_descr", "fasta_filter_by_length", - "tp_sed_tool", "hisat2", - "ncbi_blastn_wrapper", "spades", - "subtract_query1", + "tp_sed_tool", "metaspades", - "blastxml_to_top_descr", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "trimmomatic", - "tp_awk_tool", - "fasterq_dump", - "samtool_filter2" + "tp_awk_tool" ], "update_time": "2022-02-02", "versions": 28 @@ -59116,23 +74328,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", "Peak calling", + "Mapping", + "Statistical calculation", + "Primer removal", + "Sequencing quality control", "Formatting", + "Sequence composition calculation", "Gene regulatory network analysis", - "Read summarisation", - "Primer removal", + "Sequence alignment analysis", + "Validation", "Read pre-processing", "Sequence trimming", - "Mapping", - "Statistical calculation", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "1ee43d90b69829e9", @@ -59147,29 +74359,29 @@ "cut_and_run" ], "tools": [ - "deeptools_multi_bam_summary", - "bedtools_bamtobed", - "rseqc_read_distribution", - "trim_galore", - "rseqc_infer_experiment", + "deeptools_plot_correlation", "wig_to_bigWig", + "pe_histogram", + "deeptools_bam_coverage", + "bedtools_bamtobed", "fastqc", - "bamFilter", - "Extract genomic DNA 1", - "rseqc_geneBody_coverage2", - "macs2_predictd", + "rseqc_infer_experiment", + "bowtie2", "__MERGE_COLLECTION__", - "deeptools_plot_correlation", - "macs2_callpeak", - "tp_sort_header_tool", + "deeptools_multi_bam_summary", "featurecounts", + "multiqc", + "tp_sort_header_tool", + "Extract genomic DNA 1", + "macs2_predictd", "__FLATTEN__", - "deeptools_bam_coverage", + "bamFilter", "picard_MarkDuplicates", + "macs2_callpeak", "deeptools_plot_fingerprint", - "multiqc", - "bowtie2", - "pe_histogram" + "trim_galore", + "rseqc_read_distribution", + "rseqc_geneBody_coverage2" ], "update_time": "2022-02-01", "versions": 3 @@ -59179,8 +74391,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequence analysis", "Sequencing quality control" ], @@ -59195,17 +74407,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "unzip", "obi_illumina_pairend", "obi_annotate", - "obi_ngsfilter", - "unzip", "obi_stat", - "fastqc", - "ncbi_blastn_wrapper", "Filter1", - "obi_grep", + "ncbi_blastn_wrapper", + "obi_uniq", "obi_clean", - "obi_uniq" + "fastqc", + "obi_grep", + "obi_ngsfilter" ], "update_time": "2022-01-31", "versions": 0 @@ -59228,16 +74440,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "hyphy_annotate", + "hyphy_busted", "hyphy_summary", "hyphy_meme", - "hyphy_prime", - "hyphy_fade", "hyphy_bgm", + "hyphy_annotate", + "hyphy_fade", "hyphy_slac", - "hyphy_cfel", - "hyphy_busted", - "hyphy_fel" + "hyphy_prime", + "hyphy_fel", + "hyphy_cfel" ], "update_time": "2022-01-26", "versions": 1 @@ -59247,8 +74459,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Sequence motif discovery" + "Sequence motif discovery", + "Mapping" ], "edam_topic": [], "id": "d3a4e6cc1b4565e5", @@ -59264,8 +74476,8 @@ "chiara" ], "tools": [ - "__UNZIP_COLLECTION__", "bedtools_intersectbed", + "__UNZIP_COLLECTION__", "homer_findMotifsGenome" ], "update_time": "2022-01-26", @@ -59291,8 +74503,8 @@ "tags": [], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2022-01-24", "versions": 1 @@ -59317,8 +74529,8 @@ "tags": [], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2022-01-24", "versions": 3 @@ -59328,12 +74540,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read binning", - "Scaffolding", + "k-mer counting", "De-novo assembly", + "Read binning", "Genome assembly", "Phasing", - "k-mer counting" + "Scaffolding" ], "edam_topic": [], "id": "3480204a99bf4a35", @@ -59357,15 +74569,15 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Pairwise sequence alignment", - "Phasing", - "k-mer counting", - "Read binning", - "Sequence assembly validation", "Visualisation", + "Read binning", + "Genome assembly", + "Phasing", "Scaffolding", - "Genome assembly" + "Pairwise sequence alignment", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "69be0fb8276753ec", @@ -59379,9 +74591,9 @@ "tags": [], "tools": [ "minimap2", - "merqury", "quast", - "purge_dups" + "purge_dups", + "merqury" ], "update_time": "2022-01-23", "versions": 2 @@ -59427,9 +74639,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "pampa_glmcomm", "pampa_plotglm", - "pampa_communitymetrics" + "pampa_communitymetrics", + "pampa_glmcomm" ], "update_time": "2022-01-13", "versions": 2 @@ -59454,13 +74666,13 @@ "name:ebvderivedmodelled" ], "tools": [ - "interactive_tool_wallace", - "interactive_tool_rstudio", + "Filter1", + "spocc_occ", "Count1", "Summary_Statistics1", - "spocc_occ", - "Filter1", - "gdal_ogr2ogr" + "interactive_tool_wallace", + "gdal_ogr2ogr", + "interactive_tool_rstudio" ], "update_time": "2022-01-13", "versions": 9 @@ -59470,8 +74682,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "48d0dc424e71d8c2", @@ -59485,18 +74697,18 @@ "tags": [], "tools": [ "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_dada", + "tp_head_tool", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", - "dada2_learnErrors", - "dada2_dada", + "tp_tail_tool", "tp_cat", - "tp_head_tool", + "dada2_learnErrors", + "dada2_mergePairs", "tp_replace_in_column", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies", - "tp_tail_tool" + "__UNZIP_COLLECTION__" ], "update_time": "2022-01-11", "versions": 6 @@ -59508,15 +74720,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", "Scatter plot plotting", + "Sequence assembly visualisation", "Sequencing quality control", - "Pairwise sequence alignment", - "Variant calling", "Formatting", - "Sequence assembly visualisation", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Read pre-processing" + "Pairwise sequence alignment", + "Read pre-processing", + "Variant calling" ], "edam_topic": [], "id": "fc0b9efa7d2e61e6", @@ -59529,28 +74741,28 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "seq_filter_by_id", - "table_compute", - "ncbi_acc_download", - "minimap2", - "ivar_consensus", - "bandage_info", "__EXTRACT_DATASET__", - "comp1", - "bioext_bam2msa", - "samtools_stats", + "collapse_dataset", + "ncbi_blastn_wrapper", + "table_compute", + "Filter1", "sort1", "Show beginning1", - "ncbi_blastn_wrapper", - "samtools_depth", - "collapse_dataset", "ngsutils_bam_filter", + "nanoplot", "Convert characters1", + "comp1", + "tp_easyjoin_tool", + "seq_filter_by_id", + "bioext_bam2msa", + "ivar_consensus", + "ncbi_acc_download", + "minimap2", + "samtools_stats", + "bandage_info", "porechop", - "Cut1", - "nanoplot", - "Filter1" + "samtools_depth", + "Cut1" ], "update_time": "2022-01-03", "versions": 3 @@ -59601,17 +74813,17 @@ "gtn" ], "tools": [ - "xarray_metadata_info", - "graphicsmagick_image_montage", + "regexColumn1", "xarray_coords_info", "__EXTRACT_DATASET__", - "xarray_mapplot", - "ggplot2_point", - "regexColumn1", "__MERGE_COLLECTION__", + "graphicsmagick_image_montage", + "climate_stripes", "xarray_netcdf2netcdf", "xarray_select", - "climate_stripes" + "xarray_mapplot", + "ggplot2_point", + "xarray_metadata_info" ], "update_time": "2021-12-28", "versions": 83 @@ -59649,16 +74861,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", + "Sequence contamination filtering", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Sequence contamination filtering", "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "45fc2dada84d251e", @@ -59671,13 +74883,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "fastp", "ngsutils_bam_filter", "ivar_consensus", - "qualimap_bamqc", - "ivar_variants" + "fastp", + "ivar_variants", + "bwa_mem", + "bamleftalign", + "qualimap_bamqc" ], "update_time": "2021-12-21", "versions": 15 @@ -59701,18 +74913,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "circos_interval_to_text", + "param_value_from_file", "Add_a_column1", - "circos_interval_to_tile", - "tp_awk_tool", "Cut1", - "param_value_from_file", - "tp_grep_tool", + "circos_interval_to_text", + "tp_cat", "mitos2", - "circos", "tp_replace_in_column", - "fasta_compute_length", - "tp_cat" + "circos", + "circos_interval_to_tile", + "tp_grep_tool", + "tp_awk_tool", + "fasta_compute_length" ], "update_time": "2021-12-20", "versions": 26 @@ -59733,10 +74945,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "snpSift_rmInfo", - "snpSift_vcfCheck", "snpSift_filter", - "snpEff" + "snpSift_rmInfo", + "snpEff", + "snpSift_vcfCheck" ], "update_time": "2021-12-14", "versions": 5 @@ -59757,8 +74969,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "snpSift_rmInfo", "snpSift_filter", + "snpSift_rmInfo", "snpEff" ], "update_time": "2021-12-12", @@ -59769,18 +74981,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Sequence composition calculation", + "Sequence alignment analysis", + "Generation", "Genome indexing", - "Generation" + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "a08279c2a305afff", @@ -59793,14 +75005,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "samtools_flagstat", - "tp_sort_header_tool", "trimmomatic", - "bwa", + "deeptools_bam_coverage", "trim_galore", + "tp_sort_header_tool", "fastqc", - "bamFilter" + "bamFilter", + "bwa", + "samtools_flagstat" ], "update_time": "2021-12-10", "versions": 0 @@ -59823,8 +75035,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "snpSift_rmInfo", "snpSift_filter", + "snpSift_rmInfo", "snpEff" ], "update_time": "2021-12-09", @@ -59835,18 +75047,18 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Pairwise sequence alignment", - "Sequence assembly visualisation", - "Sequence assembly validation", "Visualisation", "Statistical calculation", - "Taxonomic classification", + "Genome assembly", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly" + "Sequencing quality control", + "Cross-assembly", + "Pairwise sequence alignment", + "De-novo assembly", + "Sequence composition calculation", + "Sequence assembly validation", + "Taxonomic classification" ], "edam_topic": [], "id": "8b2f53745e720d0f", @@ -59859,16 +75071,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_filter_by_length", "flye", - "porechop", + "racon", "kraken2", + "porechop", "bandage_image", "quast", - "minimap2", + "krona-text", "fastqc", - "racon", - "krona-text" + "fasta_filter_by_length", + "minimap2" ], "update_time": "2021-12-03", "versions": 1 @@ -59878,8 +75090,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome assembly", "Multilocus sequence typing", + "Genome assembly", "Antimicrobial resistance prediction", "Taxonomic classification" ], @@ -59894,11 +75106,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "abricate", "kraken2", - "mlst", "fasta-stats", - "spades" + "spades", + "abricate", + "mlst" ], "update_time": "2021-12-02", "versions": 4 @@ -59908,11 +75120,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "c7e1aee909c9b483", @@ -59925,10 +75137,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "fastq_groomer", "htseq_count", - "bowtie2" + "bowtie2", + "fastq_groomer", + "fastqc" ], "update_time": "2021-11-22", "versions": 1 @@ -59938,11 +75150,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "eb3cfa4d1f05fc0e", @@ -59955,11 +75167,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastq_groomer", "htseq_count", "tophat2", "multiqc", - "fastqc" + "fastqc", + "fastq_groomer" ], "update_time": "2021-11-21", "versions": 24 @@ -59969,11 +75181,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "cf9dc7ad34c81fa2", @@ -59986,10 +75198,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "htseq_count", + "bowtie2", "fastq_groomer", - "bowtie2" + "fastqc" ], "update_time": "2021-11-17", "versions": 8 @@ -59999,11 +75211,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "70b1c40b818cc320", @@ -60016,10 +75228,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", "htseq_count", + "bowtie2", "fastq_groomer", - "bowtie2" + "fastqc" ], "update_time": "2021-11-16", "versions": 4 @@ -60043,11 +75255,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2021-11-14", "versions": 4 @@ -60057,16 +75269,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "ce7f7c6eef526d67", @@ -60081,12 +75293,12 @@ "proteomics" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2021-11-09", "versions": 2 @@ -60096,18 +75308,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome alignment", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", "Copy number estimation", + "Sequence alignment", + "Genome alignment", + "Sequencing quality control", "Sequence visualisation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "220961d803697f54", @@ -60122,47 +75334,47 @@ "miracum" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", - "gemini_load", - "samtools_view", - "__FILTER_FROM_FILE__", - "fastqc", - "circos", - "__BUILD_LIST__", - "split_file_to_collection", "__EXTRACT_DATASET__", + "trimmomatic", + "collapse_dataset", "tp_find_and_replace", - "tp_replace_in_line", - "gemini_annotate", - "__MERGE_COLLECTION__", - "datamash_ops", + "Grep1", + "bg_column_arrange_by_header", + "fastqc", + "__APPLY_RULES__", + "add_line_to_file", + "qualimap_bamqc", + "samtools_calmd", + "param_value_from_file", "Filter1", - "tp_text_file_with_recurring_lines", "Add_a_column1", - "bamleftalign", - "datamash_transpose", - "collapse_dataset", + "__MERGE_COLLECTION__", + "multiqc", + "__BUILD_LIST__", + "__SORTLIST__", + "Convert characters1", + "tp_easyjoin_tool", + "bwa_mem", "gemini_query", - "add_line_to_file", - "param_value_from_file", + "bamleftalign", + "samtools_view", "snpEff", "compose_text_param", - "Convert characters1", - "__SORTLIST__", + "gemini_annotate", + "tp_replace_in_line", + "tp_replace_in_column", "__RELABEL_FROM_FILE__", - "__APPLY_RULES__", - "qualimap_bamqc", "varscan_somatic", - "tp_replace_in_column", - "bwa_mem", - "samtools_calmd", - "trimmomatic", - "Cut1", + "datamash_ops", "samtools_rmdup", - "multiqc", "control_freec", - "Grep1" + "gemini_load", + "datamash_transpose", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", + "circos", + "Cut1", + "__FILTER_FROM_FILE__" ], "update_time": "2021-11-09", "versions": 2 @@ -60173,8 +75385,8 @@ "doi": "", "edam_operation": [ "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" + "Phylogenetic analysis", + "Taxonomic classification" ], "edam_topic": [], "id": "5ce8a472e6e95c60", @@ -60189,13 +75401,13 @@ "metagenomics" ], "tools": [ - "combine_metaphlan2_humann2", - "humann_renorm_table", "humann_regroup_table", + "humann_rename_table", + "combine_metaphlan2_humann2", + "Grep1", "humann_unpack_pathways", "humann_split_stratified_table", - "Grep1", - "humann_rename_table" + "humann_renorm_table" ], "update_time": "2021-11-09", "versions": 8 @@ -60206,8 +75418,8 @@ "doi": "", "edam_operation": [ "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" + "Phylogenetic analysis", + "Taxonomic classification" ], "edam_topic": [], "id": "23dd2253da51e22e", @@ -60222,14 +75434,14 @@ "metagenomics" ], "tools": [ - "combine_metaphlan2_humann2", - "humann_renorm_table", - "humann", "humann_regroup_table", + "humann_rename_table", + "humann", + "combine_metaphlan2_humann2", + "Grep1", "humann_unpack_pathways", "humann_split_stratified_table", - "Grep1", - "humann_rename_table" + "humann_renorm_table" ], "update_time": "2021-11-09", "versions": 6 @@ -60239,16 +75451,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "dc438d4ae1866df8", @@ -60263,12 +75475,12 @@ "proteomics" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2021-11-09", "versions": 4 @@ -60278,11 +75490,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", "Visualisation", "Prediction and recognition", - "Formatting" + "Filtering", + "Formatting", + "Label-free quantification" ], "edam_topic": [], "id": "d0e062aee910086a", @@ -60296,17 +75508,17 @@ "tags": [], "tools": [ "msconvert", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", "regex1", + "query_tabular", "unipept", "tp_replace_in_line", + "search_gui", "Remove beginning1", - "query_tabular", + "tp_replace_in_column", "flashlfq", - "Filter1", - "tp_replace_in_column" + "Cut1", + "peptide_shaker" ], "update_time": "2021-11-09", "versions": 5 @@ -60318,9 +75530,9 @@ "edam_operation": [ "Sequence contamination filtering", "Statistical calculation", - "Read mapping", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping" ], "edam_topic": [], "id": "606a04c4aa95d010", @@ -60333,17 +75545,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "mimodd_rebase", - "bcftools_norm", - "bamleftalign", - "mimodd_varextract", - "samtools_view", + "bowtie2", "samtools_rmdup", - "mimodd_covstats", "snpEff", + "bcftools_norm", + "mimodd_covstats", + "mimodd_rebase", "fastp", - "bowtie2", - "mimodd_varcall" + "samtools_view", + "mimodd_varextract", + "mimodd_varcall", + "bamleftalign" ], "update_time": "2021-10-30", "versions": 4 @@ -60355,9 +75567,9 @@ ], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "9a52516ec0b539ea", @@ -60371,9 +75583,9 @@ "tags": [], "tools": [ "rna_star", - "featurecounts", "tp_sed_tool", - "collection_column_join" + "collection_column_join", + "featurecounts" ], "update_time": "2021-10-29", "versions": 8 @@ -60388,14 +75600,14 @@ ], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", "Mapping assembly", + "Scaffolding", "Cross-assembly", - "Transcriptome assembly" + "Transcriptome assembly", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "30b514cfb9cce524", @@ -60409,9 +75621,9 @@ "tags": [], "tools": [ "fasta-stats", + "flye", "quast", - "busco", - "flye" + "busco" ], "update_time": "2021-10-26", "versions": 8 @@ -60434,13 +75646,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2021-10-21", "versions": 1 @@ -60450,12 +75662,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Primer removal", "Read pre-processing", "Sequence trimming", + "Primer removal", "Read mapping", - "Formatting" + "Formatting", + "Data handling" ], "edam_topic": [], "id": "41b5f0d519404df7", @@ -60468,13 +75680,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", "bowtie2", "__EXTRACT_DATASET__", - "picard_MarkDuplicates", - "trim_galore", + "deeptools_bam_coverage", "fasterq_dump", - "__FLATTEN__" + "trim_galore", + "__FLATTEN__", + "picard_MarkDuplicates" ], "update_time": "2021-10-19", "versions": 18 @@ -60486,16 +75698,16 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Visualisation", "Statistical calculation", - "Taxonomic classification", + "Sequence alignment", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping", + "Taxonomic classification" ], "edam_topic": [], "id": "ee0005a5487653ba", @@ -60513,14 +75725,14 @@ "microbiome" ], "tools": [ - "Kraken2Tax", - "trimmomatic", "kraken2", + "trimmomatic", + "picard_SamToFastq", + "taxonomy_krona_chart", + "fastqc", "bwa", "samtools_view", - "taxonomy_krona_chart", - "picard_SamToFastq", - "fastqc" + "Kraken2Tax" ], "update_time": "2021-10-18", "versions": 2 @@ -60542,8 +75754,8 @@ "tags": [], "tools": [ "cat1", - "Filter1", - "gops_intersect_1" + "gops_intersect_1", + "Filter1" ], "update_time": "2021-09-28", "versions": 1 @@ -60556,11 +75768,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "57769c948e14f9ac", @@ -60577,15 +75789,15 @@ "iwc" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-09-24", "versions": 1 @@ -60597,15 +75809,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "1761092d0e7deece", @@ -60623,17 +75835,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-09-24", "versions": 1 @@ -60645,18 +75857,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "0189bab68f828d86", @@ -60673,21 +75885,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-09-24", "versions": 1 @@ -60699,16 +75911,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "476db04368d5e90c", @@ -60727,27 +75939,27 @@ "iwc" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2021-09-24", "versions": 1 @@ -60776,8 +75988,8 @@ "tools": [ "cat1", "param_value_from_file", - "quast", - "bionano_scaffold" + "bionano_scaffold", + "quast" ], "update_time": "2021-09-01", "versions": 0 @@ -60798,9 +76010,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_awk_tool", "query_tabular", - "param_value_from_file" + "param_value_from_file", + "tp_awk_tool" ], "update_time": "2021-08-31", "versions": 7 @@ -60813,19 +76025,19 @@ ], "doi": "", "edam_operation": [ - "De-novo assembly", - "Pairwise sequence alignment", - "Phasing", - "k-mer counting", - "Read binning", - "Sequence assembly validation", "Visualisation", + "Read binning", + "Genome assembly", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "Pairwise sequence alignment", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation" ], "edam_topic": [], "id": "d67299c34e63f3d9", @@ -60839,18 +76051,18 @@ "tags": [], "tools": [ "cat1", - "Add_a_column1", - "meryl", - "tp_cut_tool", - "gfa_to_fa", - "tp_find_and_replace", "param_value_from_file", - "tp_grep_tool", - "quast", + "Add_a_column1", "minimap2", + "tp_find_and_replace", "merqury", + "tp_grep_tool", + "meryl", + "gfa_to_fa", "Convert characters1", "busco", + "quast", + "tp_cut_tool", "genomescope", "cutadapt", "hifiasm", @@ -60864,15 +76076,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Read summarisation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation" ], "edam_topic": [], "id": "60a45de522b8b695", @@ -60885,11 +76097,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", "featurecounts", - "hisat2", + "trim_galore", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-08-30", "versions": 6 @@ -60899,14 +76111,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -60922,15 +76134,15 @@ "hackbiointernship2021" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "racon", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2021-08-21", "versions": 0 @@ -60940,14 +76152,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -60963,15 +76175,15 @@ "hackbiointernship2021" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "racon", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2021-08-21", "versions": 0 @@ -60981,14 +76193,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -61004,15 +76216,15 @@ "hackbiointernship2021" ], "tools": [ - "gfa_to_fa", - "bandage_image", - "nanoplot", + "miniasm", "racon", "PlasFlow", + "nanoplot", + "gfa_to_fa", + "bandage_image", + "unicycler", "minimap2", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2021-08-21", "versions": 0 @@ -61022,14 +76234,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -61045,15 +76257,15 @@ "hackbio2021internship" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "racon", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2021-08-20", "versions": 1 @@ -61082,15 +76294,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Read summarisation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation" ], "edam_topic": [], "id": "bbe2a1615c8faaae", @@ -61103,11 +76315,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", "featurecounts", - "hisat2", + "trim_galore", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-08-12", "versions": 1 @@ -61117,15 +76329,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Read summarisation", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Read mapping" ], "edam_topic": [], "id": "443ea80b36d862f5", @@ -61138,11 +76350,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", + "bowtie2", "featurecounts", + "trim_galore", "collection_column_join", - "fastqc", - "bowtie2" + "fastqc" ], "update_time": "2021-08-12", "versions": 2 @@ -61152,15 +76364,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Read summarisation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation" ], "edam_topic": [], "id": "eb8168bc01249596", @@ -61173,11 +76385,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", "featurecounts", - "hisat2", + "trim_galore", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-08-11", "versions": 0 @@ -61205,8 +76417,8 @@ ], "tools": [ "cat1", - "datamash_ops", "Remove beginning1", + "datamash_ops", "join_files_on_column_fuzzy" ], "update_time": "2021-08-09", @@ -61234,12 +76446,12 @@ "shared" ], "tools": [ - "cardinal_preprocessing", - "cardinal_filtering", - "Show beginning1", "cardinal_spectra_plots", "Filter1", - "cardinal_mz_images" + "Show beginning1", + "cardinal_filtering", + "cardinal_mz_images", + "cardinal_preprocessing" ], "update_time": "2021-08-09", "versions": 9 @@ -61266,16 +76478,16 @@ "shared" ], "tools": [ - "tp_easyjoin_tool", "cat1", - "cardinal_classification", "param_value_from_file", - "sklearn_train_test_split", + "Filter1", + "addName", + "cardinal_classification", "cardinal_filtering", - "datamash_ops", "Remove beginning1", - "addName", - "Filter1" + "tp_easyjoin_tool", + "datamash_ops", + "sklearn_train_test_split" ], "update_time": "2021-08-09", "versions": 6 @@ -61302,18 +76514,18 @@ "shared" ], "tools": [ - "tp_easyjoin_tool", "cat1", + "param_value_from_file", + "addName", + "Filter1", "cardinal_classification", + "cardinal_filtering", "Cut1", + "Remove beginning1", + "tp_easyjoin_tool", "tp_sorted_uniq", - "param_value_from_file", - "sklearn_train_test_split", "datamash_ops", - "addName", - "Remove beginning1", - "cardinal_filtering", - "Filter1" + "sklearn_train_test_split" ], "update_time": "2021-08-09", "versions": 8 @@ -61340,14 +76552,14 @@ "shared" ], "tools": [ - "cardinal_preprocessing", - "cardinal_combine", - "cardinal_data_exporter", - "maldi_quant_peak_detection", - "cardinal_filtering", "Filter1", + "cardinal_filtering", + "maldi_quant_peak_detection", "__BUILD_LIST__", - "cardinal_quality_report" + "cardinal_quality_report", + "cardinal_combine", + "cardinal_preprocessing", + "cardinal_data_exporter" ], "update_time": "2021-08-09", "versions": 9 @@ -61359,10 +76571,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "03e8b0d3dcedc092", @@ -61379,22 +76591,22 @@ "shared" ], "tools": [ - "tp_easyjoin_tool", "cat1", - "ip_scale_image", + "addName", + "datamash_ops", "ip_viz_overlay_moving_and_fixed_image", - "Cut1", - "graphicsmagick_image_convert", - "ip_projective_transformation_points", + "ip_coordinates_of_roi", "imagecoordinates_flipaxis", - "addName", + "Cut1", "tp_replace_in_line", + "tp_cat", "Remove beginning1", - "datamash_ops", - "ip_coordinates_of_roi", - "ip_landmark_registration", + "tp_easyjoin_tool", + "ip_scale_image", + "ip_projective_transformation_points", "cardinal_mz_images", - "tp_cat" + "graphicsmagick_image_convert", + "ip_landmark_registration" ], "update_time": "2021-08-09", "versions": 12 @@ -61425,16 +76637,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", - "Mapping", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Variant calling", + "Validation", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ff2fd4a4bb27d859", @@ -61449,41 +76661,41 @@ "miracum" ], "tools": [ - "tp_easyjoin_tool", - "bg_column_arrange_by_header", + "__EXTRACT_DATASET__", "snpSift_extractFields", - "gemini_load", - "samtools_view", + "trimmomatic", + "collapse_dataset", + "tp_find_and_replace", + "Grep1", + "bg_column_arrange_by_header", + "fastqc", "lofreq_call", + "add_line_to_file", + "samtools_calmd", + "Filter1", + "Add_a_column1", + "multiqc", + "__SORTLIST__", "lofreq_indelqual", - "fastqc", - "split_file_to_collection", + "tp_easyjoin_tool", + "bwa_mem", + "gemini_query", "bedtools_genomecoveragebed", - "__EXTRACT_DATASET__", - "tp_find_and_replace", - "tp_replace_in_line", - "gemini_annotate", - "datamash_ops", + "addValue", "bamleftalign", - "Add_a_column1", - "datamash_transpose", - "collapse_dataset", - "gemini_query", - "add_line_to_file", + "samtools_view", "snpEff", - "addValue", - "__SORTLIST__", - "lofreq_alnqual", + "gemini_annotate", + "tp_replace_in_line", + "bedtools_mergebed", "tp_replace_in_column", + "lofreq_alnqual", + "datamash_ops", + "datamash_transpose", + "gemini_load", "lofreq_filter", - "bwa_mem", - "samtools_calmd", - "trimmomatic", - "Cut1", - "multiqc", - "Filter1", - "Grep1", - "bedtools_mergebed" + "split_file_to_collection", + "Cut1" ], "update_time": "2021-07-29", "versions": 2 @@ -61493,12 +76705,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Genome assembly", - "Read mapping", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "db10c092fad70d69", @@ -61511,11 +76723,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "trimmomatic", - "rnaspades", "multiqc", "fastqc", - "bowtie2" + "rnaspades" ], "update_time": "2021-07-21", "versions": 1 @@ -61536,14 +76748,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "prepare_receptor", + "prepare_box", "openbabel_svg_depiction", + "openbabel_compound_convert", + "docking", "CONVERTER_SMILES_to_sdf", "chembl", - "tp_grep_tool", - "openbabel_compound_convert", - "prepare_box", - "prepare_receptor", - "docking" + "tp_grep_tool" ], "update_time": "2021-07-05", "versions": 0 @@ -61571,8 +76783,8 @@ ], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2021-06-24", "versions": 3 @@ -61582,27 +76794,27 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Phylogenetic tree analysis", + "Visualisation", + "Primer removal", "Sequencing quality control", - "Phylogenetic analysis", + "Phylogenetic tree analysis", "Formatting", - "Sequence comparison", - "Visualisation", + "Sequence similarity search", + "Species frequency estimation", + "Conversion", "Phylogenetic inference", - "Read pre-processing", "Sequence trimming", - "Phylogenetic tree visualisation", + "Statistical calculation", "Nucleic acid sequence analysis", + "Sequence comparison", + "Phylogenetic analysis", "Phylogenetic tree editing", - "Species frequency estimation", "Sequence composition calculation", - "Statistical calculation", - "Primer removal", - "Taxonomic classification", - "Validation" + "Read pre-processing", + "Sequence alignment analysis", + "Validation", + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "a8f829deb69b30ab", @@ -61617,27 +76829,27 @@ "asaim" ], "tools": [ - "combine_metaphlan2_humann2", - "graphlan", "humann", + "combine_metaphlan2_humann2", + "Grep1", "fastq_paired_end_interlacer", - "taxonomy_krona_chart", + "humann_unpack_pathways", "fastqc", - "humann_rename_table", "metaphlan", - "group_humann2_uniref_abundances_to_go", - "graphlan_annotate", - "bg_sortmerna", - "humann_renorm_table", + "humann_regroup_table", + "humann_rename_table", + "multiqc", "humann2_genefamilies_genus_level", + "group_humann2_uniref_abundances_to_go", + "cutadapt", "export2graphlan", + "bg_sortmerna", + "taxonomy_krona_chart", + "graphlan_annotate", + "graphlan", "Cut1", "format_metaphlan2_output", - "humann_regroup_table", - "humann_unpack_pathways", - "multiqc", - "Grep1", - "cutadapt" + "humann_renorm_table" ], "update_time": "2021-06-24", "versions": 14 @@ -61650,17 +76862,17 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Gene-set enrichment analysis", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Transcriptome assembly", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "7136ce9f18c74853", @@ -61695,19 +76907,19 @@ "quality" ], "tools": [ - "volcanoplot", + "Filter1", "rna_star", - "tp_cut_tool", - "deseq2", + "goenrichment", "trim_galore", - "join1", - "Filter1", + "qualimap_rnaseq", "Remove beginning1", - "goenrichment", + "volcanoplot", + "join1", "fastqc", - "qualimap_bamqc", + "tp_cut_tool", "stringtie", - "qualimap_rnaseq" + "deseq2", + "qualimap_bamqc" ], "update_time": "2021-06-21", "versions": 10 @@ -61717,16 +76929,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", + "Statistical calculation", "Genetic variation analysis", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Statistical calculation", + "Sequence composition calculation", "Sequence analysis", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "b3b094f1bdbaa04a", @@ -61739,15 +76951,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "freebayes", + "samtool_filter2", + "samtools_rmdup", "bcftools_norm", - "bwa_mem", "snpEff_download", - "gemini_load", - "samtools_rmdup", "snpEff", - "freebayes", - "samtool_filter2", + "gemini_load", "gemini_inheritance", + "bwa_mem", "fastqc" ], "update_time": "2021-06-19", @@ -61758,16 +76970,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", + "Statistical calculation", "Genetic variation analysis", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Statistical calculation", + "Sequence composition calculation", "Sequence analysis", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "b82a4065be048ef6", @@ -61780,15 +76992,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "freebayes", + "samtool_filter2", + "samtools_rmdup", "bcftools_norm", - "bwa_mem", "snpEff_download", - "gemini_load", - "samtools_rmdup", "snpEff", - "freebayes", - "samtool_filter2", + "gemini_load", "gemini_inheritance", + "bwa_mem", "fastqc" ], "update_time": "2021-06-19", @@ -61814,12 +77026,12 @@ "computational-chemistry" ], "tools": [ - "gmx_editconf", - "get_pdb", "gmx_solvate", - "tp_grep_tool", + "gmx_setup", + "get_pdb", "gmx_em", - "gmx_setup" + "gmx_editconf", + "tp_grep_tool" ], "update_time": "2021-06-16", "versions": 2 @@ -61841,8 +77053,8 @@ "tags": [], "tools": [ "get_pdb", - "gmx_em", - "gmx_setup" + "gmx_setup", + "gmx_em" ], "update_time": "2021-06-16", "versions": 7 @@ -61868,12 +77080,12 @@ "fates" ], "tools": [ - "xarray_metadata_info", "ctsm_fates", "__EXTRACT_DATASET__", - "ggplot2_point", "tp_find_and_replace", - "xarray_select" + "xarray_select", + "ggplot2_point", + "xarray_metadata_info" ], "update_time": "2021-06-15", "versions": 5 @@ -61898,16 +77110,16 @@ "computational-chemistry" ], "tools": [ - "ambertools_acpype", - "gmx_editconf", - "get_pdb", "gmx_solvate", - "tp_grep_tool", - "gmx_sim", + "gmx_setup", "gmx_merge_topology_files", + "ambertools_acpype", + "get_pdb", "openbabel_compound_convert", "gmx_em", - "gmx_setup" + "gmx_editconf", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2021-06-14", "versions": 0 @@ -61979,9 +77191,9 @@ "ont" ], "tools": [ + "datamash_reverse", "tp_replace_in_line", "taxonomy_krona_chart", - "datamash_reverse", "kraken2" ], "update_time": "2021-06-10", @@ -61993,12 +77205,12 @@ "doi": "", "edam_operation": [ "DNA mapping", + "Genetic variation analysis", "Sequence alignment analysis", - "Local alignment", + "Sequence analysis", "Sequence alignment", - "Genetic variation analysis", "Global alignment", - "Sequence analysis" + "Local alignment" ], "edam_topic": [], "id": "04a4dcac3fd922c5", @@ -62011,12 +77223,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "fastq_to_fasta_python", + "samtools_fastx", + "EMBOSS: trimest102", "filter_by_fasta_ids", "ngmlr", - "EMBOSS: trimest102", - "samtools_fastx", - "trimmer", - "fastq_to_fasta_python" + "trimmer" ], "update_time": "2021-06-09", "versions": 3 @@ -62040,9 +77252,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "unipept", - "query_tabular", "search_gui", + "query_tabular", + "unipept", "peptide_shaker" ], "update_time": "2021-05-29", @@ -62053,14 +77265,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Phylogenetic tree analysis", "Visualisation", + "Nucleic acid sequence analysis", + "Phylogenetic tree editing", + "Phylogenetic tree analysis", + "Conversion", "Phylogenetic inference", - "Taxonomic classification", "Phylogenetic tree visualisation", - "Nucleic acid sequence analysis", - "Phylogenetic tree editing" + "Taxonomic classification" ], "edam_topic": [], "id": "19de5cbae7f48103", @@ -62075,12 +77287,12 @@ "metagenomics" ], "tools": [ - "metaphlan", + "export2graphlan", "graphlan_annotate", - "Cut1", - "graphlan", "taxonomy_krona_chart", - "export2graphlan" + "graphlan", + "metaphlan", + "Cut1" ], "update_time": "2021-05-25", "versions": 2 @@ -62090,14 +77302,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence comparison", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence comparison", + "Sequence similarity search", + "Sequence composition calculation", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", "Validation" ], @@ -62115,8 +77327,8 @@ ], "tools": [ "bg_sortmerna", - "fastq_paired_end_interlacer", "multiqc", + "fastq_paired_end_interlacer", "fastqc", "cutadapt" ], @@ -62166,8 +77378,8 @@ "covid19.galaxyproject.org" ], "tools": [ - "__ZIP_COLLECTION__", - "collapse_dataset" + "collapse_dataset", + "__ZIP_COLLECTION__" ], "update_time": "2021-05-21", "versions": 3 @@ -62177,8 +77389,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "e764c594f070f107", @@ -62192,9 +77404,9 @@ "tags": [], "tools": [ "cat1", - "deseq2", + "deg_annotate", "Filter1", - "deg_annotate" + "deseq2" ], "update_time": "2021-05-18", "versions": 0 @@ -62215,17 +77427,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_split_on_column", - "fasta2tab", - "table_compute", - "collapse_dataset", - "join1", - "tab2fasta", - "trimmer", - "sort1", "ncbi_makeblastdb", + "Filter1", + "sort1", + "collapse_dataset", "ncbi_blastn_wrapper", - "Filter1" + "tab2fasta", + "table_compute", + "fasta2tab", + "join1", + "tp_split_on_column", + "trimmer" ], "update_time": "2021-05-11", "versions": 9 @@ -62246,11 +77458,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", - "pepquery", + "Filter1", "Remove beginning1", + "pepquery", "Grouping1", - "Filter1" + "Cut1" ], "update_time": "2021-05-10", "versions": 7 @@ -62271,11 +77483,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", - "pepquery", + "Filter1", "Remove beginning1", + "pepquery", "Grouping1", - "Filter1" + "Cut1" ], "update_time": "2021-05-10", "versions": 4 @@ -62300,15 +77512,15 @@ "tags": [], "tools": [ "msconvert", - "fasta_merge_files_and_filter_unique_sequences", + "Filter1", + "query_tabular", + "Grep1", "search_gui", - "peptide_shaker", - "Cut1", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "Grep1" + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "peptide_shaker" ], "update_time": "2021-05-04", "versions": 4 @@ -62332,11 +77544,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "unipept", "pepquery", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2021-04-30", "versions": 8 @@ -62346,12 +77558,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", + "Genome indexing", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "ddd604341afd9cf7", @@ -62366,11 +77578,11 @@ "miracum" ], "tools": [ - "bwa_mem", "trimmomatic", "vcfcombine", - "strelka_somatic", "multiqc", + "bwa_mem", + "strelka_somatic", "qualimap_bamqc" ], "update_time": "2021-04-29", @@ -62392,17 +77604,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_split_on_column", - "fasta2tab", - "table_compute", - "collapse_dataset", - "join1", - "tab2fasta", - "trimmer", - "sort1", "ncbi_makeblastdb", + "Filter1", + "sort1", + "collapse_dataset", "ncbi_blastn_wrapper", - "Filter1" + "tab2fasta", + "table_compute", + "fasta2tab", + "join1", + "tp_split_on_column", + "trimmer" ], "update_time": "2021-04-28", "versions": 22 @@ -62425,13 +77637,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", "Cut1", - "datamash_ops", "Remove beginning1", - "bg_uniq", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops", + "bg_uniq" ], "update_time": "2021-04-25", "versions": 1 @@ -62453,11 +77665,11 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", - "tp_cut_tool", "sort1", - "addValue", - "Filter1" + "tp_cut_tool", + "addValue" ], "update_time": "2021-04-24", "versions": 1 @@ -62483,14 +77695,14 @@ "single-cell" ], "tools": [ + "anndata_import", "scanpy_plot", "anndata_manipulate", - "anndata_import", "scanpy_inspect", - "scanpy_filter", "scanpy_normalize", + "scanpy_remove_confounders", "scanpy_cluster_reduce_dimension", - "scanpy_remove_confounders" + "scanpy_filter" ], "update_time": "2021-04-24", "versions": 33 @@ -62514,12 +77726,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "ncbi_makeblastdb", + "muscle", "fasttree", - "ncbi_acc_download", - "tp_cut_tool", "ncbi_blastp_wrapper", - "ncbi_makeblastdb", - "muscle" + "tp_cut_tool", + "ncbi_acc_download" ], "update_time": "2021-04-23", "versions": 4 @@ -62541,8 +77753,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "spring_map", - "collapse_dataset" + "collapse_dataset", + "spring_map" ], "update_time": "2021-04-23", "versions": 9 @@ -62552,9 +77764,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", + "Sequence contamination filtering", "Sequencing quality control", - "Sequence contamination filtering" + "Read mapping" ], "edam_topic": [], "id": "0882300f7b399587", @@ -62570,18 +77782,18 @@ "mapping-by-sequencing" ], "tools": [ - "mimodd_rebase", - "__ZIP_COLLECTION__", "bowtie2", - "vcfvcfintersect", - "mimodd_vcf_filter", - "mimodd_info", "snpEff", - "mimodd_map", + "mimodd_info", + "mimodd_rebase", "fastp", + "__BUILD_LIST__", + "vcfvcfintersect", + "__ZIP_COLLECTION__", "tp_text_file_with_recurring_lines", - "__RELABEL_FROM_FILE__", - "__BUILD_LIST__" + "mimodd_vcf_filter", + "mimodd_map", + "__RELABEL_FROM_FILE__" ], "update_time": "2021-04-17", "versions": 21 @@ -62614,17 +77826,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Differential gene expression analysis", - "Sequencing quality control", "Sequence alignment", - "Visualisation", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", "Transcriptome assembly", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "68e8042f11d5a3fd", @@ -62637,27 +77849,27 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_multijoin_tool", - "volcanoplot", + "trimmomatic", "table_compute", + "tp_cat", + "join1", "fastqc", - "tp_cut_tool", - "hisat2", - "deseq2", + "ggplot2_point", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "ggplot2_pca", - "join1", "featurecounts", + "multiqc", + "tp_multijoin_tool", + "tp_sort_header_tool", "stringtie", + "deseq2", + "ggplot2_pca", "tp_replace_in_column", - "ggplot2_heatmap2", - "trimmomatic", - "ggplot2_point", + "hisat2", + "volcanoplot", "Remove beginning1", - "multiqc", - "Filter1", - "tp_cat" + "tp_cut_tool", + "ggplot2_heatmap2" ], "update_time": "2021-04-10", "versions": 0 @@ -62682,12 +77894,12 @@ "tags": [], "tools": [ "tab2fasta", - "Cut1", "unipept", "ncbi_blastp_wrapper", "pepquery", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2021-04-07", "versions": 3 @@ -62711,16 +77923,16 @@ "moleculardynamics" ], "tools": [ - "ambertools_acpype", - "gmx_editconf", - "get_pdb", "gmx_solvate", - "tp_grep_tool", - "gmx_sim", + "gmx_setup", "gmx_merge_topology_files", + "ambertools_acpype", + "get_pdb", "openbabel_compound_convert", "gmx_em", - "gmx_setup" + "gmx_editconf", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2021-04-06", "versions": 12 @@ -62730,17 +77942,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Gene expression analysis", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "2d2d0c2231babc50", @@ -62757,22 +77969,22 @@ "arabidopsis" ], "tools": [ + "Filter1", + "targetfinder", + "__MERGE_COLLECTION__", + "tp_find_and_replace", + "salmon", + "multiqc", + "rbc_mirdeep2_quantifier", + "trim_galore", + "rbc_mirdeep2_mapper", "tp_sort_header_tool", "filter_by_fasta_ids", + "fastqc", "tp_cut_tool", "Cut1", - "tp_find_and_replace", - "trim_galore", - "rbc_mirdeep2_mapper", - "salmon", - "__MERGE_COLLECTION__", - "targetfinder", - "Filter1", "bg_uniq", - "multiqc", - "fastqc", - "deseq2", - "rbc_mirdeep2_quantifier" + "deseq2" ], "update_time": "2021-04-01", "versions": 25 @@ -62801,9 +78013,9 @@ "reads" ], "tools": [ + "sistr_cmd", "tp_cat", - "shovill", - "sistr_cmd" + "shovill" ], "update_time": "2021-03-30", "versions": 3 @@ -62813,14 +78025,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Sequence composition calculation", - "Taxonomic classification", + "Statistical calculation", + "Visualisation", + "Genome assembly", + "Sequence assembly validation", "Sequencing quality control", - "Genome assembly" + "Aggregation", + "Taxonomic classification" ], "edam_topic": [], "id": "b2b46e71046b1999", @@ -62833,14 +78045,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Kraken2Tax", - "trimmomatic", "kraken2", - "quast", - "taxonomy_krona_chart", + "trimmomatic", "fastqc", + "taxonomy_krona_chart", + "quast", + "unicycler", "staramr_search", - "unicycler" + "Kraken2Tax" ], "update_time": "2021-03-25", "versions": 2 @@ -62866,9 +78078,9 @@ "random" ], "tools": [ - "tp_awk_tool", "collection_element_identifiers", - "__RELABEL_FROM_FILE__" + "__RELABEL_FROM_FILE__", + "tp_awk_tool" ], "update_time": "2021-03-18", "versions": 9 @@ -62892,19 +78104,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "uniprotxml_downloader", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2021-03-17", "versions": 6 @@ -62914,11 +78126,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "e5f6d12e08d7a13b", @@ -62931,9 +78143,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", + "htseq_count", "bowtie2", - "htseq_count" + "fastqc" ], "update_time": "2021-03-17", "versions": 1 @@ -62954,8 +78166,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", "split_file_to_collection", + "cat1", "Remove beginning1", "tp_text_file_with_recurring_lines" ], @@ -62978,26 +78190,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_ops", - "scanpy_read_10x", - "__BUILD_LIST__", - "scanpy_run_umap", + "scanpy_find_markers", "scanpy_filter_genes", - "scanpy_parameter_iterator", - "__MERGE_COLLECTION__", - "tp_replace_in_line", - "_ensembl_gtf2gene_list", + "scanpy_normalise_data", + "scanpy_compute_graph", "scanpy_integrate_harmony", + "__MERGE_COLLECTION__", + "__BUILD_LIST__", "scanpy_find_variable_genes", - "__FILTER_FAILED_DATASETS__", - "scanpy_compute_graph", - "scanpy_plot_embed", + "scanpy_filter_cells", + "scanpy_run_umap", "scanpy_run_tsne", - "scanpy_find_markers", - "scanpy_find_cluster", + "_ensembl_gtf2gene_list", + "tp_replace_in_line", "scanpy_run_pca", - "scanpy_normalise_data", - "scanpy_filter_cells" + "scanpy_find_cluster", + "scanpy_read_10x", + "anndata_ops", + "scanpy_parameter_iterator", + "__FILTER_FAILED_DATASETS__", + "scanpy_plot_embed" ], "update_time": "2021-03-15", "versions": 1 @@ -63020,14 +78232,14 @@ "wfdemo" ], "tools": [ + "samtools_stats", + "Filter1", "collapse_dataset", + "compose_text_param", "Cut1", - "__FILTER_FROM_FILE__", "samtools_view", "tp_grep_tool", - "samtools_stats", - "compose_text_param", - "Filter1" + "__FILTER_FROM_FILE__" ], "update_time": "2021-03-10", "versions": 4 @@ -63052,10 +78264,10 @@ "tools": [ "collection_element_identifiers", "tp_find_and_replace", - "__FILTER_FROM_FILE__", + "__BUILD_LIST__", "tp_text_file_with_recurring_lines", "__RELABEL_FROM_FILE__", - "__BUILD_LIST__" + "__FILTER_FROM_FILE__" ], "update_time": "2021-03-10", "versions": 1 @@ -63078,22 +78290,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", "anndata_ops", - "join1", "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "scanpy_run_umap", "scanpy_find_markers", "scanpy_run_pca", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_run_umap" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2021-03-10", "versions": 2 @@ -63116,21 +78328,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", "anndata_ops", - "join1", - "scanpy_compute_graph", - "Cut1", "scanpy_plot_embed", - "scanpy_run_tsne", + "scanpy_run_umap", "scanpy_find_markers", "scanpy_run_pca", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_run_umap" + "Cut1", + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2021-03-10", "versions": 1 @@ -63154,12 +78366,12 @@ "covid19.galaxyproject.org" ], "tools": [ - "bg_column_arrange_by_header", - "Cut1", - "tp_unfold_column_tool", + "Filter1", "compose_text_param", "split_file_to_collection", - "Filter1" + "tp_unfold_column_tool", + "bg_column_arrange_by_header", + "Cut1" ], "update_time": "2021-03-06", "versions": 8 @@ -63184,9 +78396,9 @@ "abramis" ], "tools": [ + "Grep1", "cat1", - "tp_head_tool", - "Grep1" + "tp_head_tool" ], "update_time": "2021-03-03", "versions": 2 @@ -63196,8 +78408,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Quantification", "Image analysis", + "Quantification", "Parsing" ], "edam_topic": [], @@ -63213,18 +78425,18 @@ "cellprofiler" ], "tools": [ - "cp_common", - "cp_export_to_spreadsheet", - "cp_save_images", - "cp_measure_object_size_shape", - "cp_track_objects", - "cp_identify_primary_objects", - "cp_overlay_outlines", "unzip", - "cp_measure_object_intensity", + "cp_save_images", "cp_cellprofiler", + "cp_export_to_spreadsheet", + "cp_measure_object_intensity", "cp_tile", - "cp_color_to_gray" + "cp_track_objects", + "cp_overlay_outlines", + "cp_common", + "cp_color_to_gray", + "cp_measure_object_size_shape", + "cp_identify_primary_objects" ], "update_time": "2021-03-02", "versions": 7 @@ -63246,8 +78458,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "get_pdb", - "param_value_from_file" + "param_value_from_file", + "get_pdb" ], "update_time": "2021-02-26", "versions": 2 @@ -63270,20 +78482,20 @@ "ecology" ], "tools": [ - "datamash_transpose", - "tp_sort_header_tool", "regexColumn1", - "Count1", - "pampa_presabs", - "regex1", - "tp_cut_tool", "pampa_glmsp", "pampa_plotglm", - "pampa_communitymetrics", - "mergeCols1", "Filter1", + "datamash_transpose", + "pampa_presabs", + "regex1", "pampa_glmcomm", - "tp_cat" + "tp_cat", + "pampa_communitymetrics", + "tp_sort_header_tool", + "Count1", + "tp_cut_tool", + "mergeCols1" ], "update_time": "2021-02-24", "versions": 0 @@ -63333,11 +78545,11 @@ "name:galaxyp" ], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2021-02-09", "versions": 3 @@ -63347,8 +78559,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "fe6c64676be56ee9", @@ -63361,8 +78573,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-02-06", "versions": 0 @@ -63372,13 +78584,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "31d9eb6a120411d6", @@ -63393,9 +78605,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-02-06", "versions": 0 @@ -63416,11 +78628,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-02-06", "versions": 0 @@ -63441,11 +78653,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-02-04", "versions": 1 @@ -63455,9 +78667,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "f0209559f3686fcc", @@ -63470,8 +78682,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-02-04", "versions": 0 @@ -63481,9 +78693,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "e6c5ae57528918d2", @@ -63517,11 +78729,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-28", "versions": 0 @@ -63531,13 +78743,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "a35e0c2fcba4e95f", @@ -63552,9 +78764,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-28", "versions": 0 @@ -63564,9 +78776,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "39bf638cd7b56fd6", @@ -63579,8 +78791,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-01-28", "versions": 0 @@ -63590,8 +78802,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "2f7c04ad219a9d2d", @@ -63604,8 +78816,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-01-28", "versions": 0 @@ -63630,10 +78842,10 @@ "name:gtn" ], "tools": [ - "pep_pointer", + "peptide_genomic_coordinate", "query_tabular", "ncbi_blastp_wrapper", - "peptide_genomic_coordinate" + "pep_pointer" ], "update_time": "2021-01-27", "versions": 2 @@ -63643,12 +78855,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "a7638e7f908fd90d", @@ -63665,23 +78877,23 @@ "name:gtn" ], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "gffcompare", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", - "filter_tabular", "sqlite_to_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "stringtie", + "hisat2", + "bed_to_protein_map" ], "update_time": "2021-01-27", "versions": 3 @@ -63691,8 +78903,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "2a7e63d1cc583002", @@ -63709,11 +78921,11 @@ "name:gtn" ], "tools": [ - "search_gui", - "peptide_shaker", + "mz_to_sqlite", "tab2fasta", + "search_gui", "query_tabular", - "mz_to_sqlite" + "peptide_shaker" ], "update_time": "2021-01-27", "versions": 4 @@ -63734,11 +78946,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-24", "versions": 0 @@ -63748,13 +78960,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "1b49eda539658e53", @@ -63769,9 +78981,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-24", "versions": 0 @@ -63781,13 +78993,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "54467870b7c635f2", @@ -63802,9 +79014,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-24", "versions": 0 @@ -63825,11 +79037,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-24", "versions": 0 @@ -63862,9 +79074,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "db63d53712d2571b", @@ -63877,8 +79089,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-01-24", "versions": 0 @@ -63888,8 +79100,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6d47a24218d08930", @@ -63902,8 +79114,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-01-24", "versions": 1 @@ -63913,9 +79125,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "2aac571c44e6a7c8", @@ -63928,8 +79140,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-01-24", "versions": 0 @@ -63950,11 +79162,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2021-01-24", "versions": 0 @@ -63964,13 +79176,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "d1338e2b4002a364", @@ -63985,9 +79197,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-24", "versions": 0 @@ -63997,8 +79209,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3386856a60b35897", @@ -64011,8 +79223,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-01-24", "versions": 0 @@ -64033,11 +79245,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-21", "versions": 0 @@ -64058,11 +79270,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-20", "versions": 0 @@ -64072,9 +79284,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "e47351e2edd93a1a", @@ -64087,8 +79299,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-01-20", "versions": 0 @@ -64098,13 +79310,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "de3eafbcf42c75bb", @@ -64119,9 +79331,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-20", "versions": 0 @@ -64131,8 +79343,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "f9ddc4dd9140b293", @@ -64145,8 +79357,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-01-20", "versions": 0 @@ -64156,23 +79368,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", + "Genome assembly", + "Sequence alignment", + "Sequence assembly visualisation", "Mapping assembly", + "Sequencing quality control", + "Sequence file editing", + "Cross-assembly", + "Pairwise sequence alignment", "De-novo assembly", + "Generation", + "Genome indexing", "Sequence composition calculation", "Read mapping", - "Sequencing quality control", - "Pairwise sequence alignment", - "Sequence alignment", - "Sequence assembly visualisation", "Genome visualisation", - "Sequence file editing", - "Sequence contamination filtering", - "Genome assembly", - "Statistical calculation", - "Genome indexing", - "Generation", - "Cross-assembly" + "Data handling" ], "edam_topic": [], "id": "d2f75f70c33394ee", @@ -64185,21 +79397,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bandage_info", + "flye", + "seqtk_sample", + "spades", "deeptools_bam_coverage", - "bwa_mem", + "fastp", "sam_merge2", + "bandage_image", + "bwa_mem", + "fastqc", "fasta_merge_files_and_filter_unique_sequences", "fasta_filter_by_length", - "sam_pileup", - "flye", - "bandage_image", - "seqtk_sample", "minimap2", - "fastp", "jbrowse", - "fastqc", - "spades", - "bandage_info" + "sam_pileup" ], "update_time": "2021-01-20", "versions": 2 @@ -64220,9 +79432,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "pep_pointer", + "peptide_genomic_coordinate", "query_tabular", - "peptide_genomic_coordinate" + "pep_pointer" ], "update_time": "2021-01-18", "versions": 1 @@ -64232,8 +79444,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "0aee7ffa5f6384bd", @@ -64246,16 +79458,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fasta2tab", - "search_gui", - "peptide_shaker", - "Cut1", + "query_tabular", "tab2fasta", "ncbi_blastp_wrapper", + "fasta2tab", + "search_gui", "Convert characters1", "Grouping1", "mz_to_sqlite", - "query_tabular" + "Cut1", + "peptide_shaker" ], "update_time": "2021-01-18", "versions": 1 @@ -64265,12 +79477,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "39afbf843b5513bf", @@ -64283,21 +79495,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gffcompare", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "translate_bed", - "tp_replace_in_line", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", "sqlite_to_tabular", + "tp_replace_in_line", + "tp_cat", "stringtie", + "translate_bed", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "gffcompare", + "hisat2", + "bed_to_protein_map" ], "update_time": "2021-01-18", "versions": 3 @@ -64307,8 +79519,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene set testing", "Gene functional annotation", + "Gene set testing", "Gene-set enrichment analysis" ], "edam_topic": [], @@ -64322,13 +79534,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "fgsea", "Add_a_column1", - "egsea", "tp_sort_header_tool", + "egsea", + "join1", "tp_cut_tool", "Cut1", - "join1", - "fgsea", "goseq" ], "update_time": "2021-01-15", @@ -64339,8 +79551,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "227d97974573aaf2", @@ -64353,8 +79565,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "limma_voom", - "annotatemyids" + "annotatemyids", + "limma_voom" ], "update_time": "2021-01-15", "versions": 0 @@ -64364,13 +79576,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "ab6e6ffaaebab45b", @@ -64385,9 +79597,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2021-01-15", "versions": 0 @@ -64408,11 +79620,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-01-15", "versions": 0 @@ -64422,9 +79634,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "bd74a116e3f8d5b8", @@ -64437,8 +79649,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-01-15", "versions": 0 @@ -64463,8 +79675,8 @@ "tags": [], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2021-01-15", "versions": 5 @@ -64474,14 +79686,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Primer removal", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Differential gene expression analysis", - "Sequence alignment", - "RNA-Seq quantification" + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d72edb9f8c529f47", @@ -64494,9 +79706,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "trim_galore", - "featurecounts", "Filter1", + "featurecounts", + "trim_galore", "hisat2", "deseq2" ], @@ -64521,21 +79733,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", "cat1", - "anndata_manipulate", + "Filter1", "anndata_import", "scanpy_plot", - "tp_awk_tool", + "tp_tail_tool", "Cut1", - "scanpy_filter", + "anndata_manipulate", "scanpy_inspect", "scanpy_normalize", - "scanpy_cluster_reduce_dimension", "scanpy_remove_confounders", - "Filter1", "tp_replace_in_column", - "tp_tail_tool" + "scanpy_cluster_reduce_dimension", + "scanpy_filter", + "anndata_inspect", + "tp_awk_tool" ], "update_time": "2021-01-07", "versions": 1 @@ -64556,10 +79768,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "stoceps_glm", "stoceps_maketablecarrer", - "stoceps_trend_indic", - "stoceps_filteringsp" + "stoceps_glm", + "stoceps_filteringsp", + "stoceps_trend_indic" ], "update_time": "2021-01-06", "versions": 1 @@ -64569,15 +79781,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "2a39dbc8fc6dd5d3", @@ -64596,22 +79808,22 @@ "fastq->vcf" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", + "__FILTER_FROM_FILE__", + "samtools_stats", + "Filter1", "collapse_dataset", + "lofreq_viterbi", "snpeff_sars_cov_2", "Cut1", - "samtools_view", - "__FILTER_FROM_FILE__", - "tp_grep_tool", - "samtools_stats", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "Filter1" + "lofreq_filter", + "lofreq_indelqual", + "bwa_mem", + "lofreq_call", + "tp_grep_tool", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-01-06", "versions": 1 @@ -64635,11 +79847,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "gatk4_mutect2", - "picard_MarkDuplicates", + "picard_AddOrReplaceReadGroups", "picard_SortSam", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2021-01-02", "versions": 3 @@ -64662,11 +79874,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "varscan_mpileup", + "bowtie2", "samtools_mpileup", - "samtools_view", "samtools_sort", - "bowtie2" + "varscan_mpileup", + "samtools_view" ], "update_time": "2021-01-02", "versions": 4 @@ -64689,10 +79901,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", + "samtools_mpileup", "bowtie2", - "samtools_view", - "samtools_mpileup" + "samtools_sort", + "samtools_view" ], "update_time": "2021-01-01", "versions": 3 @@ -64716,12 +79928,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", + "Filter1", "unipept", "pepquery", - "query_tabular", "Grouping1", - "Filter1" + "query_tabular", + "Cut1" ], "update_time": "2020-12-28", "versions": 3 @@ -64731,10 +79943,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "02700454f57eb556", @@ -64748,12 +79960,12 @@ "tags": [], "tools": [ "msconvert", - "Cut1", + "Filter1", "unipept", "pepquery", - "query_tabular", "Grouping1", - "Filter1" + "query_tabular", + "Cut1" ], "update_time": "2020-12-21", "versions": 11 @@ -64763,19 +79975,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence assembly visualisation", - "Genome visualisation", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", + "Visualisation", "Statistical calculation", "Genome assembly", + "Sequence assembly visualisation", + "Sequencing quality control", "Coding region prediction", - "Validation" + "Sequence composition calculation", + "Sequence assembly validation", + "Validation", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "7aa32aba3fde0708", @@ -64788,17 +80000,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "CONVERTER_bz2_to_uncompressed", "bowtie2", + "prokka", + "CONVERTER_bz2_to_uncompressed", "trimmomatic", + "multiqc", "bandage_image", "quast", - "multiqc", - "jbrowse", - "shovill", - "prokka", "fastqc", - "staramr_search" + "jbrowse", + "staramr_search", + "shovill" ], "update_time": "2020-12-17", "versions": 1 @@ -64808,11 +80020,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", + "Differential gene expression analysis", "Sequence trimming", - "RNA-Seq analysis", - "Differential gene expression analysis" + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "02a212cc9f134570", @@ -64830,13 +80042,13 @@ "differential-expression" ], "tools": [ - "Cut1", + "Filter1", + "rbc_mirdeep2", + "rbc_mirdeep2_quantifier", "trim_galore", "rbc_mirdeep2_mapper", - "rbc_mirdeep2", - "Filter1", - "deseq2", - "rbc_mirdeep2_quantifier" + "Cut1", + "deseq2" ], "update_time": "2020-12-17", "versions": 0 @@ -64846,10 +80058,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "5e4774036aa20b80", @@ -64862,20 +80074,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 1 @@ -64885,10 +80097,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "f0bec337f9998289", @@ -64901,20 +80113,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 5 @@ -64924,10 +80136,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "41df8c7821b5f2fc", @@ -64940,20 +80152,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 1 @@ -64963,10 +80175,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "3e01a2c6d954ae6e", @@ -64979,20 +80191,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 3 @@ -65013,8 +80225,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_awk_tool", - "query_tabular" + "query_tabular", + "tp_awk_tool" ], "update_time": "2020-12-13", "versions": 1 @@ -65035,8 +80247,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_awk_tool", - "query_tabular" + "query_tabular", + "tp_awk_tool" ], "update_time": "2020-12-13", "versions": 5 @@ -65046,10 +80258,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "82b6871682f1659a", @@ -65062,20 +80274,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 1 @@ -65085,10 +80297,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "9ef76d764d9961b2", @@ -65101,20 +80313,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-13", "versions": 7 @@ -65135,8 +80347,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_awk_tool", - "query_tabular" + "query_tabular", + "tp_awk_tool" ], "update_time": "2020-12-13", "versions": 1 @@ -65146,8 +80358,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d6f7e86d52d43555", @@ -65160,11 +80372,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "ggplot2_heatmap2", - "table_compute", "Filter1", "tp_head_tool", + "table_compute", + "tp_easyjoin_tool", + "ggplot2_heatmap2", "deseq2" ], "update_time": "2020-12-11", @@ -65186,8 +80398,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", - "random_lines1" + "random_lines1", + "cat1" ], "update_time": "2020-12-09", "versions": 2 @@ -65208,11 +80420,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "dropletutils_read_10x", - "scpred_preprocess_data", - "scpred_get_std_output", "scpred_predict_labels", - "ct_combine_tool_outputs" + "scpred_preprocess_data", + "dropletutils_read_10x", + "ct_combine_tool_outputs", + "scpred_get_std_output" ], "update_time": "2020-12-07", "versions": 0 @@ -65233,10 +80445,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "dropletutils_read_10x", "scmap_scmap_cluster", - "scmap_preprocess_sce", + "dropletutils_read_10x", "ct_combine_tool_outputs", + "scmap_preprocess_sce", "scmap_get_std_output" ], "update_time": "2020-12-07", @@ -65258,10 +80470,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "scmap_scmap_cell", "dropletutils_read_10x", "ct_combine_tool_outputs", "scmap_preprocess_sce", - "scmap_scmap_cell", "scmap_get_std_output" ], "update_time": "2020-12-07", @@ -65283,8 +80495,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "garnett_train_classifier", - "monocle3_create" + "monocle3_create", + "garnett_train_classifier" ], "update_time": "2020-12-07", "versions": 0 @@ -65305,10 +80517,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scmap_select_features", - "dropletutils_read_10x", "scmap_preprocess_sce", - "scmap_index_cell" + "scmap_select_features", + "scmap_index_cell", + "dropletutils_read_10x" ], "update_time": "2020-12-07", "versions": 0 @@ -65329,10 +80541,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scmap_select_features", - "dropletutils_read_10x", "scmap_index_cluster", - "scmap_preprocess_sce" + "scmap_preprocess_sce", + "scmap_select_features", + "dropletutils_read_10x" ], "update_time": "2020-12-07", "versions": 0 @@ -65353,10 +80565,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "scpred_preprocess_data", + "dropletutils_read_10x", "scpred_train_model", "scpred_eigen_decompose", - "dropletutils_read_10x", - "scpred_preprocess_data", "scpred_get_feature_space" ], "update_time": "2020-12-07", @@ -65378,8 +80590,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "garnett_classify_cells", "garnett_get_std_output", + "garnett_classify_cells", "ct_combine_tool_outputs", "monocle3_create" ], @@ -65402,11 +80614,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2020-12-07", "versions": 1 @@ -65427,11 +80639,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2020-12-07", "versions": 1 @@ -65441,10 +80653,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "612dc5bdf388585f", @@ -65457,21 +80669,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", + "Filter1", "cat1", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-12-05", "versions": 5 @@ -65481,11 +80693,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -65502,13 +80714,13 @@ "transcriptomics" ], "tools": [ - "chira_extract", + "chira_quantify", "chira_collapse", - "chira_merge", "chira_map", - "query_tabular", + "chira_extract", + "chira_merge", "fastqc", - "chira_quantify", + "query_tabular", "cutadapt" ], "update_time": "2020-12-04", @@ -65519,23 +80731,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence composition calculation", - "Sequence similarity search", + "Visualisation", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence comparison", - "Visualisation", + "Sequence similarity search", + "Conversion", "Phylogenetic inference", + "Sequence trimming", "Statistical calculation", - "Primer removal", - "Taxonomic classification", + "Sequence comparison", + "Phylogenetic tree editing", + "Sequence composition calculation", "Read pre-processing", - "Phylogenetic tree visualisation", - "Sequence trimming", + "Sequence alignment analysis", "Validation", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "dfc2c53ac3103eff", @@ -65550,27 +80762,27 @@ "asaim" ], "tools": [ + "humann2_renorm_table", "combine_metaphlan2_humann2", - "graphlan", + "Grep1", "fastq_paired_end_interlacer", - "taxonomy_krona_chart", - "fastqc", - "group_humann2_uniref_abundances_to_go", "metaphlan2krona", + "fastqc", + "humann2", + "multiqc", "metaphlan2", - "graphlan_annotate", - "humann2_renorm_table", - "Grouping1", - "bg_sortmerna", - "tp_sort_header_tool", + "group_humann2_uniref_abundances_to_go", "humann2_genefamilies_genus_level", - "humann2", + "tp_sort_header_tool", + "cutadapt", "export2graphlan", + "bg_sortmerna", + "taxonomy_krona_chart", "humann2_unpack_pathways", - "format_metaphlan2_output", - "multiqc", - "Grep1", - "cutadapt" + "graphlan_annotate", + "graphlan", + "Grouping1", + "format_metaphlan2_output" ], "update_time": "2020-12-04", "versions": 1 @@ -65580,21 +80792,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Scatter plot plotting", - "De-novo assembly", - "Sequencing quality control", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome visualisation", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", + "Visualisation", "Genome assembly", - "Coding region prediction", + "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly" + "Sequencing quality control", + "Cross-assembly", + "Box-Whisker plot plotting", + "Coding region prediction", + "De-novo assembly", + "Sequence assembly validation", + "Genome visualisation", + "Filtering" ], "edam_topic": [], "id": "4ddbffe4b3fef275", @@ -65609,17 +80821,17 @@ "assembly" ], "tools": [ - "CONVERTER_bz2_to_uncompressed", + "prokka", "flye", - "filtlong", - "bandage_image", + "jbrowse", "nanoplot", + "bandage_image", + "Grep1", "quast", - "jbrowse", - "prokka", + "filtlong", "tbl2gff3", "staramr_search", - "Grep1" + "CONVERTER_bz2_to_uncompressed" ], "update_time": "2020-12-03", "versions": 6 @@ -65629,10 +80841,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "08cfb9b21c1ec808", @@ -65645,12 +80857,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", - "umi_tools_dedup", - "cshl_fastx_renamer", "featurecounts", - "umi_tools_count", - "umi_tools_extract" + "cshl_fastx_renamer", + "umi_tools_extract", + "umi_tools_dedup", + "rna_star", + "umi_tools_count" ], "update_time": "2020-11-30", "versions": 3 @@ -65660,10 +80872,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "d4b3da4cc5a50044", @@ -65676,12 +80888,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", - "umi_tools_dedup", - "cshl_fastx_renamer", "featurecounts", - "umi_tools_count", - "umi_tools_extract" + "cshl_fastx_renamer", + "umi_tools_extract", + "umi_tools_dedup", + "rna_star", + "umi_tools_count" ], "update_time": "2020-11-30", "versions": 8 @@ -65691,8 +80903,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Pairwise sequence alignment" + "Pairwise sequence alignment", + "Mapping" ], "edam_topic": [], "id": "d4a6fb334f5dd10e", @@ -65706,8 +80918,8 @@ "tags": [], "tools": [ "minimap2", - "flair_correct", "bedtools_bamtobed", + "flair_correct", "flair_collapse" ], "update_time": "2020-11-30", @@ -65733,15 +80945,15 @@ "tags": [], "tools": [ "msconvert", - "fasta_merge_files_and_filter_unique_sequences", + "Filter1", + "query_tabular", + "Grep1", "search_gui", - "peptide_shaker", - "Cut1", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "Grep1" + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "peptide_shaker" ], "update_time": "2020-11-24", "versions": 4 @@ -65766,12 +80978,12 @@ "tags": [], "tools": [ "tab2fasta", - "Cut1", "unipept", "ncbi_blastp_wrapper", "pepquery", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2020-11-24", "versions": 2 @@ -65796,12 +81008,12 @@ "tags": [], "tools": [ "tab2fasta", - "Cut1", "unipept", "ncbi_blastp_wrapper", "pepquery", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2020-11-24", "versions": 3 @@ -65826,12 +81038,12 @@ "tags": [], "tools": [ "tab2fasta", - "Cut1", "unipept", "ncbi_blastp_wrapper", "pepquery", + "Grouping1", "query_tabular", - "Grouping1" + "Cut1" ], "update_time": "2020-11-23", "versions": 3 @@ -65853,8 +81065,8 @@ "tags": [], "tools": [ "cat1", - "Filter1", - "gops_intersect_1" + "gops_intersect_1", + "Filter1" ], "update_time": "2020-11-20", "versions": 0 @@ -65875,10 +81087,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", - "table_compute", + "column_remove_by_header", "anndata_manipulate", - "column_remove_by_header" + "anndata_inspect", + "table_compute" ], "update_time": "2020-11-19", "versions": 3 @@ -65921,20 +81133,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "retrieve_scxa", - "scanpy_compute_graph", - "scanpy_read_10x", + "scmap_scmap_cell", "scmap_scmap_cluster", + "scanpy_read_10x", + "retrieve_scxa", + "scanpy_find_cluster", "sceasy_convert", - "scmap_preprocess_sce", "scanpy_run_pca", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scmap_scmap_cell", - "scanpy_find_cluster", + "scanpy_filter_genes", + "scmap_preprocess_sce", "scanpy_scale_data", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-11-05", "versions": 3 @@ -65944,11 +81156,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -65965,13 +81177,13 @@ "transcriptomics" ], "tools": [ - "chira_extract", + "chira_quantify", "chira_collapse", - "chira_merge", "chira_map", - "query_tabular", + "chira_extract", + "chira_merge", "fastqc", - "chira_quantify", + "query_tabular", "cutadapt" ], "update_time": "2020-11-03", @@ -65982,11 +81194,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -66003,13 +81215,13 @@ "transcriptomics" ], "tools": [ - "chira_extract", + "chira_quantify", "chira_collapse", - "chira_merge", "chira_map", - "query_tabular", + "chira_extract", + "chira_merge", "fastqc", - "chira_quantify", + "query_tabular", "cutadapt" ], "update_time": "2020-11-03", @@ -66054,20 +81266,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ucsc_cell_browser", - "hca_matrix_downloader", - "scanpy_compute_graph", "scanpy_read_10x", "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_find_markers", - "scanpy_run_pca", "scanpy_run_umap", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", + "ucsc_cell_browser", "scanpy_scale_data", + "scanpy_find_variable_genes", + "hca_matrix_downloader", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-10-26", "versions": 3 @@ -66091,20 +81303,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "cat1", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-10-09", "versions": 8 @@ -66114,10 +81326,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Prediction and recognition", "Visualisation", - "Formatting", - "Prediction and recognition" + "Filtering", + "Formatting" ], "edam_topic": [], "id": "6cb85fe1ad0c9f3b", @@ -66130,21 +81342,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "uniprotxml_downloader", "msconvert", + "Filter1", "cat1", - "fasta_merge_files_and_filter_unique_sequences", - "search_gui", - "peptide_shaker", - "Cut1", + "query_tabular", "unipept", - "pepquery", + "Cut1", + "Grep1", + "search_gui", "Remove beginning1", - "query_tabular", + "pepquery", "Grouping1", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "Filter1", - "Grep1", - "uniprotxml_downloader" + "peptide_shaker" ], "update_time": "2020-10-06", "versions": 1 @@ -66154,8 +81366,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Quantification", "Image analysis", + "Quantification", "Parsing" ], "edam_topic": [], @@ -66172,26 +81384,26 @@ "cellprofiler" ], "tools": [ - "cp_measure_image_area_occupied", + "cp_display_data_on_image", + "idr_download_by_ids", + "cp_relate_objects", + "cp_measure_object_size_shape", "cp_measure_granularity", "cp_export_to_spreadsheet", + "cp_mask_image", "cp_measure_object_intensity", + "cp_measure_texture", + "cp_common", + "cp_image_math", + "cp_gray_to_color", "cp_measure_image_intensity", - "cp_relate_objects", "cp_measure_image_quality", - "cp_image_math", "cp_identify_primary_objects", - "idr_download_by_ids", + "cp_measure_image_area_occupied", + "cp_save_images", "cp_cellprofiler", - "cp_measure_texture", - "cp_display_data_on_image", - "cp_gray_to_color", - "cp_measure_object_size_shape", "cp_enhance_or_suppress_features", - "cp_common", - "cp_save_images", - "cp_convert_objects_to_image", - "cp_mask_image" + "cp_convert_objects_to_image" ], "update_time": "2020-10-05", "versions": 70 @@ -66216,8 +81428,8 @@ "tags": [], "tools": [ "msconvert", - "encyclopedia_quantify", - "encyclopedia_searchtolib" + "encyclopedia_searchtolib", + "encyclopedia_quantify" ], "update_time": "2020-10-02", "versions": 2 @@ -66227,10 +81439,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", "Sequencing quality control", - "Box-Whisker plot plotting", - "Scatter plot plotting" + "Scatter plot plotting", + "Filtering", + "Box-Whisker plot plotting" ], "edam_topic": [], "id": "c3bfedf33bb00069", @@ -66268,20 +81480,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scanpy_compute_graph", "scanpy_read_10x", - "scanpy_parameter_iterator", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot_embed", "_ensembl_gtf2gene_list", - "scanpy_run_tsne", + "scanpy_parameter_iterator", "scanpy_find_markers", - "scanpy_run_pca", "scanpy_run_umap", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-09-30", "versions": 0 @@ -66302,8 +81514,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "pepquery", - "query_tabular" + "query_tabular", + "pepquery" ], "update_time": "2020-09-21", "versions": 0 @@ -66313,19 +81525,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Sequencing quality control", - "Local alignment", - "Sequence alignment", + "Sequence contamination filtering", "Genome assembly", + "Sequence alignment", "Sequence assembly visualisation", - "Genome visualisation", - "Sequence contamination filtering", + "Sequencing quality control", + "Local alignment", "Sequence file editing", + "Sequence alignment analysis", + "Sequence analysis", "Global alignment", - "Sequence analysis" + "Read mapping", + "Genome visualisation", + "Data handling" ], "edam_topic": [], "id": "93d1035a307fe63d", @@ -66338,21 +81550,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "fasta_merge_files_and_filter_unique_sequences", - "ncbi_acc_download", - "filter_by_fasta_ids", - "bandage_image", - "EMBOSS: megamerger53", + "bowtie2", + "seqtk_mergefa", + "bandage_info", "samtools_stats", + "EMBOSS: megamerger53", + "spades", + "deeptools_bam_coverage", "fastp", + "bandage_image", + "filter_by_fasta_ids", "CONVERTER_bam_to_bigwig_0", - "seqtk_mergefa", - "rseqc_bam_stat", + "ncbi_acc_download", + "fasta_merge_files_and_filter_unique_sequences", "jbrowse", - "spades", - "bowtie2", - "bandage_info" + "rseqc_bam_stat" ], "update_time": "2020-09-11", "versions": 0 @@ -66402,15 +81614,15 @@ "tags": [], "tools": [ "msconvert", - "fasta_merge_files_and_filter_unique_sequences", + "Filter1", + "query_tabular", + "Grep1", "search_gui", - "peptide_shaker", - "Cut1", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "Grep1" + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "peptide_shaker" ], "update_time": "2020-09-03", "versions": 11 @@ -66435,15 +81647,15 @@ "tags": [], "tools": [ "msconvert", - "fasta_merge_files_and_filter_unique_sequences", + "Filter1", + "query_tabular", + "Grep1", "search_gui", - "peptide_shaker", - "Cut1", "pepquery", - "query_tabular", "Grouping1", - "Filter1", - "Grep1" + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "peptide_shaker" ], "update_time": "2020-09-01", "versions": 3 @@ -66471,12 +81683,12 @@ "covid19.galaxyproject.org" ], "tools": [ - "deeptools_bam_coverage", - "filter_by_fasta_ids", "picard_NormalizeFasta", "samtools_fastx", - "samtools_view", - "minimap2" + "deeptools_bam_coverage", + "filter_by_fasta_ids", + "minimap2", + "samtools_view" ], "update_time": "2020-08-30", "versions": 7 @@ -66504,19 +81716,19 @@ ], "tools": [ "cat1", - "collapse_dataset", - "Cut1", - "samtools_view", "param_value_from_file", "createInterval", "__MERGE_COLLECTION__", - "tp_text_file_with_recurring_lines", - "__RELABEL_FROM_FILE__", "tp_head_tool", - "split_file_to_collection", + "collapse_dataset", + "bedtools_intersectbed", "__BUILD_LIST__", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", "tp_replace_in_column", - "bedtools_intersectbed" + "Cut1", + "__RELABEL_FROM_FILE__", + "samtools_view" ], "update_time": "2020-08-30", "versions": 12 @@ -66556,11 +81768,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Visualisation", - "Taxonomic classification", "Pairwise sequence alignment", - "Box-Whisker plot plotting" + "Visualisation", + "Scatter plot plotting", + "Box-Whisker plot plotting", + "Taxonomic classification" ], "edam_topic": [], "id": "57cfe5062c8e01bf", @@ -66573,15 +81785,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "datamash_reverse", "kraken2", - "Cut1", - "join1", - "nanoplot", + "mergeCols1", "tp_replace_in_line", - "minimap2", "taxonomy_krona_chart", - "mergeCols1", - "datamash_reverse" + "nanoplot", + "join1", + "minimap2", + "Cut1" ], "update_time": "2020-08-03", "versions": 4 @@ -66606,10 +81818,10 @@ "glm" ], "tools": [ - "pampa_glmcomm", "pampa_glmsp", "pampa_communitymetrics", - "pampa_presabs" + "pampa_presabs", + "pampa_glmcomm" ], "update_time": "2020-07-24", "versions": 3 @@ -66632,13 +81844,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "xarray_metadata_info", "Add_a_column1", + "cds_essential_variability", + "xarray_select", "ggplot2_point", - "tp_awk_tool", + "xarray_metadata_info", "datamash_ops", - "cds_essential_variability", - "xarray_select" + "tp_awk_tool" ], "update_time": "2020-07-23", "versions": 3 @@ -66663,12 +81875,12 @@ "tags": [], "tools": [ "msconvert", - "search_gui", - "peptide_shaker", - "msms_extractor", "Show beginning1", + "msms_extractor", + "tp_cat", "Grep1", - "tp_cat" + "search_gui", + "peptide_shaker" ], "update_time": "2020-07-16", "versions": 4 @@ -66693,9 +81905,9 @@ "tags": [], "tools": [ "msconvert", + "peptide_shaker", "msms_extractor", - "search_gui", - "peptide_shaker" + "search_gui" ], "update_time": "2020-07-16", "versions": 6 @@ -66732,10 +81944,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Post-translation modification site prediction", - "k-mer counting", "PolyA signal detection", - "Genotyping" + "Genotyping", + "k-mer counting", + "Post-translation modification site prediction" ], "edam_topic": [], "id": "778923dd04996e07", @@ -66764,9 +81976,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "1e2d27fae8a41ac1", @@ -66779,13 +81991,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "dropletutils_empty_drops" ], "update_time": "2020-07-14", "versions": 9 @@ -66808,10 +82020,10 @@ "metagenomics" ], "tools": [ - "group_humann2_uniref_abundances_to_go", "humann2_renorm_table", + "humann2", "humann2_unpack_pathways", - "humann2" + "group_humann2_uniref_abundances_to_go" ], "update_time": "2020-07-14", "versions": 1 @@ -66839,15 +82051,15 @@ "name:publish" ], "tools": [ - "samtools_fastx", - "Cut1", - "samtools_view", - "minimap2", "fastq_filter", + "samtools_fastx", "samtools_merge", + "tp_cat", "split_file_to_collection", "ont_fast5_api_fast5_subset", - "tp_cat" + "minimap2", + "Cut1", + "samtools_view" ], "update_time": "2020-07-10", "versions": 16 @@ -66873,8 +82085,8 @@ ], "tools": [ "tombo_text_output", - "tombo_detect_modifications", - "tombo_resquiggle" + "tombo_resquiggle", + "tombo_detect_modifications" ], "update_time": "2020-07-08", "versions": 35 @@ -66884,12 +82096,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Post-translation modification site prediction", - "k-mer counting", "PolyA signal detection", - "Collapsing methods", + "Genotyping", + "k-mer counting", "Methylation analysis", - "Genotyping" + "Post-translation modification site prediction", + "Collapsing methods" ], "edam_topic": [], "id": "77db45ad90b4033d", @@ -66906,11 +82118,11 @@ "name:drs" ], "tools": [ - "tp_awk_tool", "nanopolishcomp_eventaligncollapse", - "nanocompore_db", "nanocompore_sampcomp", - "nanopolish_eventalign" + "nanopolish_eventalign", + "nanocompore_db", + "tp_awk_tool" ], "update_time": "2020-07-08", "versions": 28 @@ -66920,15 +82132,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", "Transcriptome assembly", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "94bbf8fa7c1f030d", @@ -66941,12 +82153,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_sort_header_tool", - "rna_star", + "Filter1", "featurecounts", "multiqc", + "tp_sort_header_tool", "fastqc", - "Filter1", + "rna_star", "stringtie" ], "update_time": "2020-07-03", @@ -66974,10 +82186,10 @@ "ralf" ], "tools": [ - "dropletutils", - "rna_starsolo", "anndata_manipulate", - "anndata_import" + "anndata_import", + "dropletutils", + "rna_starsolo" ], "update_time": "2020-06-30", "versions": 4 @@ -66998,10 +82210,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "humann2_regroup_table", + "humann2_renorm_table", "humann2_rename_table", "humann2_join_tables", - "humann2_renorm_table" + "humann2_regroup_table" ], "update_time": "2020-06-30", "versions": 1 @@ -67011,9 +82223,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", "Pairwise sequence alignment", - "Formatting" + "Formatting", + "Mapping" ], "edam_topic": [], "id": "82a60d94d699efbf", @@ -67030,17 +82242,17 @@ "name:drs" ], "tools": [ - "deeptools_bam_coverage", - "filter_by_fasta_ids", "picard_NormalizeFasta", - "samtools_fastx", - "Cut1", - "samtools_view", "createInterval", - "minimap2", + "samtools_fastx", "samtools_merge", + "deeptools_bam_coverage", "__BUILD_LIST__", - "bedtools_intersectbed" + "bedtools_intersectbed", + "filter_by_fasta_ids", + "minimap2", + "Cut1", + "samtools_view" ], "update_time": "2020-06-29", "versions": 28 @@ -67052,8 +82264,8 @@ "edam_operation": [ "Loading", "Community profiling", - "Differential gene expression analysis", - "Sequence alignment" + "Sequence alignment", + "Differential gene expression analysis" ], "edam_topic": [], "id": "b5627201bb4f6943", @@ -67068,10 +82280,10 @@ "ralf" ], "tools": [ - "dropletutils", "scanpy_filter", - "rna_starsolo", - "anndata_import" + "anndata_import", + "dropletutils", + "rna_starsolo" ], "update_time": "2020-06-29", "versions": 1 @@ -67095,9 +82307,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "iedb_api", "seq2hla", - "custom_pro_db", - "iedb_api" + "custom_pro_db" ], "update_time": "2020-06-25", "versions": 23 @@ -67107,18 +82319,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", "Gene prediction", - "Sequence contamination filtering", "Genome annotation", + "Sequence contamination filtering", "Statistical calculation", + "Visualisation", + "Genome assembly", + "Sequence assembly visualisation", + "Sequencing quality control", + "Aggregation", "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation", "Validation" ], "edam_topic": [], @@ -67140,15 +82352,15 @@ "illumina" ], "tools": [ - "bandage_image", - "quast", - "fastp", - "multiqc", "prokka", + "bandage_info", "fastqc", - "staramr_search", + "fastp", + "multiqc", + "bandage_image", + "quast", "unicycler", - "bandage_info" + "staramr_search" ], "update_time": "2020-06-24", "versions": 4 @@ -67158,24 +82370,24 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Visualisation", + "Gene prediction", + "Genome annotation", "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Genome assembly", - "Filtering", - "Aggregation", "Scatter plot plotting", + "Sequence assembly visualisation", + "Sequencing quality control", + "Box-Whisker plot plotting", + "Aggregation", + "Coding region prediction", "Sequence composition calculation", + "Pairwise sequence alignment", "Sequence assembly validation", - "Gene prediction", - "Genome annotation", - "Statistical calculation", - "Mapping", - "Coding region prediction", - "Validation" + "Validation", + "Filtering", + "Mapping" ], "edam_topic": [], "id": "ecf48fa50af560a0", @@ -67196,21 +82408,21 @@ "prokka" ], "tools": [ - "bedtools_genomecoveragebed", - "filtlong", - "Summary_Statistics1", - "bandage_image", - "nanoplot", - "quast", + "prokka", + "bandage_info", + "unicycler", "Cut1", - "minimap2", - "fastp", "multiqc", - "prokka", + "fastp", + "nanoplot", + "bandage_image", + "Summary_Statistics1", + "quast", "fastqc", - "staramr_search", - "unicycler", - "bandage_info" + "filtlong", + "minimap2", + "bedtools_genomecoveragebed", + "staramr_search" ], "update_time": "2020-06-24", "versions": 13 @@ -67220,20 +82432,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Aggregation", + "Gene prediction", + "Genome annotation", + "Visualisation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", + "Aggregation", + "Coding region prediction", + "Pairwise sequence alignment", "Sequence assembly validation", - "Visualisation", - "Gene prediction", - "Genome annotation", - "Genome assembly", - "Mapping", - "Coding region prediction" + "Filtering", + "Mapping" ], "edam_topic": [], "id": "ea485dbabc76488d", @@ -67254,18 +82466,18 @@ "coverage" ], "tools": [ - "bedtools_genomecoveragebed", - "filtlong", - "Summary_Statistics1", - "bandage_image", + "prokka", + "bandage_info", + "Cut1", "nanoplot", + "bandage_image", + "Summary_Statistics1", "quast", - "Cut1", - "minimap2", - "prokka", - "staramr_search", "unicycler", - "bandage_info" + "filtlong", + "minimap2", + "bedtools_genomecoveragebed", + "staramr_search" ], "update_time": "2020-06-24", "versions": 3 @@ -67275,10 +82487,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "64bb7a64877034dc", @@ -67293,16 +82505,16 @@ "massspectrometryimaging" ], "tools": [ - "ip_scale_image", + "addName", "ip_viz_overlay_moving_and_fixed_image", - "graphicsmagick_image_convert", - "ip_projective_transformation_points", "imagecoordinates_flipaxis", - "addName", + "tp_cat", "Remove beginning1", + "ip_scale_image", + "ip_projective_transformation_points", "ip_coordinates_of_roi", - "ip_landmark_registration", - "tp_cat" + "graphicsmagick_image_convert", + "ip_landmark_registration" ], "update_time": "2020-06-22", "versions": 11 @@ -67327,9 +82539,9 @@ "name:drs" ], "tools": [ + "ont_fast5_api_compress_fast5", "ont_fast5_api_fast5_subset", - "ont_fast5_api_multi_to_single_fast5", - "ont_fast5_api_compress_fast5" + "ont_fast5_api_multi_to_single_fast5" ], "update_time": "2020-06-19", "versions": 6 @@ -67339,15 +82551,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "b02d90c32dc67730", @@ -67360,22 +82572,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "cat1", - "gatk4_mutect2", - "bwa_mem", - "picard_MarkDuplicates", - "snpSift_extractFields", - "samtools_fastx", - "snpEff_build_gb", - "fasterq_dump", "snpEff", "samtool_filter2", + "snpSift_extractFields", + "samtools_fastx", + "gatk4_mutect2", + "multiqc", "fastp", + "fasterq_dump", + "picard_AddOrReplaceReadGroups", "vcfallelicprimitives", + "bwa_mem", "picard_SortSam", - "multiqc", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "snpEff_build_gb", + "picard_MarkDuplicates" ], "update_time": "2020-06-18", "versions": 21 @@ -67399,8 +82611,8 @@ "covid19.galaxyproject.org" ], "tools": [ - "__MERGE_COLLECTION__", - "collapse_dataset" + "collapse_dataset", + "__MERGE_COLLECTION__" ], "update_time": "2020-06-11", "versions": 6 @@ -67410,21 +82622,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", - "Formatting", "Peak calling", - "Visualisation", - "Gene regulatory network analysis", "Statistical calculation", + "Visualisation", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Read pre-processing", - "Mapping", - "Sequence trimming" + "Data handling", + "Sequence trimming", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "02655d0e4af0ee0d", @@ -67439,22 +82651,22 @@ "atac-seq" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_plot_heatmap", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_awk_tool", - "pygenomeTracks", - "samtools_sort", + "macs2_callpeak", + "picard_CollectInsertSizeMetrics", "wig_to_bigWig", - "bedtools_sortbed", + "samtools_sort", + "deeptools_plot_heatmap", "genrich", - "fastqc", + "bedtools_sortbed", "deeptools_compute_matrix", - "macs2_callpeak", + "bedtools_bamtobed", + "fastqc", "bamFilter", - "cutadapt" + "cutadapt", + "pygenomeTracks", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2020-06-10", "versions": 3 @@ -67464,14 +82676,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Mapping assembly", + "Pairwise sequence alignment", "De-novo assembly", - "Genome assembly", + "Sequence assembly visualisation", "Sequence analysis", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation" + "Genome assembly", + "Scatter plot plotting", + "Mapping assembly", + "Box-Whisker plot plotting" ], "edam_topic": [], "id": "b4de76c0a4d0e23a", @@ -67484,16 +82696,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastq_groomer", + "miniasm", + "racon", "trimmomatic", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "staramr_search", "minimap2", - "PlasFlow", - "miniasm", - "racon" + "staramr_search", + "fastq_groomer" ], "update_time": "2020-06-10", "versions": 3 @@ -67517,15 +82729,15 @@ "tags": [], "tools": [ "scanpy_plot", - "scanpy_regress_variable", - "scanpy_compute_graph", "scanpy_run_umap", "scanpy_run_pca", - "scanpy_find_variable_genes", - "scanpy_normalise_data", + "scanpy_filter_genes", "scanpy_scale_data", + "scanpy_find_variable_genes", + "scanpy_regress_variable", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-05-29", "versions": 1 @@ -67547,9 +82759,9 @@ "tags": [], "tools": [ "monocle3_topmarkers", + "monocle3_reduceDim", "monocle3_partition", - "monocle3_plotCells", - "monocle3_reduceDim" + "monocle3_plotCells" ], "update_time": "2020-05-29", "versions": 1 @@ -67559,9 +82771,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "f944ad0c35d1a472", @@ -67575,13 +82787,13 @@ "tags": [], "tools": [ "cat1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "dropletutils_empty_drops" ], "update_time": "2020-05-29", "versions": 1 @@ -67608,9 +82820,9 @@ "transcriptomics" ], "tools": [ + "umi_tools_extract", "seq_filter_by_id", - "fastqc", - "umi_tools_extract" + "fastqc" ], "update_time": "2020-05-24", "versions": 1 @@ -67621,8 +82833,8 @@ "doi": "", "edam_operation": [ "Read pre-processing", - "Sequence visualisation", - "Sequencing quality control" + "Sequencing quality control", + "Sequence visualisation" ], "edam_topic": [], "id": "f055b8fa294d4be8", @@ -67638,10 +82850,10 @@ "single-cell" ], "tools": [ - "scater_create_qcmetric_ready_sce", - "scater_plot_pca", "scater_plot_dist_scatter", - "scater_filter" + "scater_plot_pca", + "scater_filter", + "scater_create_qcmetric_ready_sce" ], "update_time": "2020-05-24", "versions": 1 @@ -67668,9 +82880,9 @@ "ml" ], "tools": [ + "ggplot2_point", "sklearn_numeric_clustering", - "csv_to_tabular", - "ggplot2_point" + "csv_to_tabular" ], "update_time": "2020-05-23", "versions": 1 @@ -67695,12 +82907,12 @@ "ml" ], "tools": [ + "sklearn_searchcv", + "plotly_regression_performance_plots", + "sklearn_generalized_linear", "sklearn_build_pipeline", "sklearn_ensemble", - "sklearn_generalized_linear", - "Remove beginning1", - "sklearn_searchcv", - "plotly_regression_performance_plots" + "Remove beginning1" ], "update_time": "2020-05-23", "versions": 1 @@ -67726,14 +82938,14 @@ "cheminformatics" ], "tools": [ + "sklearn_searchcv", + "sklearn_generalized_linear", "sklearn_build_pipeline", - "sklearn_svm_classifier", "sklearn_ensemble", - "sklearn_generalized_linear", + "plotly_ml_performance_plots", "sklearn_nn_classifier", + "sklearn_svm_classifier", "Remove beginning1", - "sklearn_searchcv", - "plotly_ml_performance_plots", "sklearn_estimator_attributes" ], "update_time": "2020-05-23", @@ -67755,8 +82967,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 2 @@ -67777,8 +82989,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 5 @@ -67799,8 +83011,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67821,8 +83033,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67843,8 +83055,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67865,8 +83077,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67887,8 +83099,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67909,8 +83121,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67931,8 +83143,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67953,8 +83165,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67975,8 +83187,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -67997,8 +83209,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68019,8 +83231,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68041,8 +83253,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68063,8 +83275,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68085,8 +83297,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68107,8 +83319,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68129,8 +83341,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68151,8 +83363,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68173,8 +83385,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68195,8 +83407,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68217,8 +83429,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68239,8 +83451,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68261,8 +83473,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68283,8 +83495,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 2 @@ -68305,8 +83517,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 2 @@ -68327,8 +83539,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68349,8 +83561,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68371,8 +83583,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 5 @@ -68393,8 +83605,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68415,8 +83627,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68437,8 +83649,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68459,8 +83671,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68481,8 +83693,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 5 @@ -68503,8 +83715,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68525,8 +83737,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68547,8 +83759,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68569,8 +83781,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68591,8 +83803,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68613,8 +83825,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68635,8 +83847,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68657,8 +83869,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 2 @@ -68679,8 +83891,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68701,8 +83913,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68723,8 +83935,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68745,8 +83957,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68767,8 +83979,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68789,8 +84001,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68811,8 +84023,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68833,8 +84045,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68855,8 +84067,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -68877,8 +84089,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68899,8 +84111,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 5 @@ -68921,8 +84133,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 1 @@ -68943,8 +84155,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 2 @@ -68965,8 +84177,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 4 @@ -68987,8 +84199,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-05-19", "versions": 3 @@ -69009,20 +84221,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scanpy_compute_graph", "scanpy_read_10x", - "scanpy_parameter_iterator", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot_embed", "_ensembl_gtf2gene_list", - "scanpy_run_tsne", + "scanpy_parameter_iterator", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-05-15", "versions": 1 @@ -69043,8 +84255,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "__MERGE_COLLECTION__", - "collapse_dataset" + "collapse_dataset", + "__MERGE_COLLECTION__" ], "update_time": "2020-05-08", "versions": 0 @@ -69054,14 +84266,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "a4e3667f6879bfaf", @@ -69074,21 +84286,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", - "bwa_mem", - "varscan_mpileup", + "bowtie2", "samtools_mpileup", + "cat1", + "snpEff", + "samtool_filter2", "snpSift_extractFields", "samtools_fastx", - "snpEff_build_gb", - "fasterq_dump", - "snpEff", "samtools_sort", - "samtool_filter2", "fastp", - "vcfallelicprimitives", + "fasterq_dump", "multiqc", - "bowtie2" + "varscan_mpileup", + "vcfallelicprimitives", + "bwa_mem", + "snpEff_build_gb" ], "update_time": "2020-05-08", "versions": 15 @@ -69098,28 +84310,28 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "De-novo assembly", - "Sequence annotation", - "de Novo sequencing", - "Formatting", - "Differential gene expression analysis", - "Sequencing quality control", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", "Database search", - "Sequence profile generation", "Format validation", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", "Sequence database search", + "Sequence profile generation", + "Probabilistic sequence generation", "Gene prediction", "Statistical calculation", - "Coding region prediction", - "Multiple sequence alignment", - "Validation" + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Sequence annotation", + "Sequence generation", + "De-novo assembly", + "Data retrieval", + "Validation", + "Data handling" ], "edam_topic": [], "id": "5be158931abca947", @@ -69132,20 +84344,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "hmmer_jackhmmer", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", + "cufflinks", "gffread", - "transdecoder", - "ncbi_blastp_wrapper", - "fasterq_dump", + "hmmer_jackhmmer", "tophat2", "antismash", "fastp", - "glimmer_knowlegde-based", - "ncbi_makeblastdb", - "glimmer_build-icm", - "cufflinks", + "fasterq_dump", "multiqc", - "uniprotxml_downloader", + "ncbi_blastp_wrapper", + "transdecoder", + "glimmer_knowlegde-based", "cuffmerge" ], "update_time": "2020-05-08", @@ -69156,33 +84368,33 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "De-novo assembly", - "de Novo sequencing", - "Formatting", - "Sequencing quality control", - "Differential gene expression analysis", - "Data retrieval", "Sequence contamination filtering", - "Genome assembly", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", - "Aggregation", "Format validation", - "Read mapping", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Aggregation", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", + "Sequence profile generation", + "Probabilistic sequence generation", + "Read mapping", "Gene prediction", "Statistical calculation", - "Coding region prediction", - "Multiple sequence alignment", - "Validation" + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Genome assembly", + "Sequence generation", + "De-novo assembly", + "Generation", + "Genome indexing", + "Data retrieval", + "Validation", + "Data handling" ], "edam_topic": [], "id": "24eaa682897379c8", @@ -69195,22 +84407,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", "hmmer_jackhmmer", - "picard_MergeSamFiles", - "transdecoder", - "samtools_fastx", - "ncbi_blastp_wrapper", - "fasterq_dump", - "unicycler", "samtool_filter2", - "fastp", + "samtools_fastx", + "picard_MergeSamFiles", "antismash", - "ncbi_makeblastdb", - "glimmer_build-icm", - "glimmer_knowlegde-based", + "fastp", + "fasterq_dump", "multiqc", - "uniprotxml_downloader" + "ncbi_blastp_wrapper", + "transdecoder", + "bwa_mem", + "unicycler", + "glimmer_knowlegde-based" ], "update_time": "2020-05-06", "versions": 26 @@ -69220,34 +84432,34 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", - "Sequence annotation", - "De-novo assembly", - "de Novo sequencing", - "Formatting", - "Sequencing quality control", - "Differential gene expression analysis", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", "Format validation", - "Read mapping", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Transcriptome assembly", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", - "RNA-Seq analysis", + "Sequence profile generation", + "Probabilistic sequence generation", + "Data handling", + "Read mapping", "Gene prediction", "Statistical calculation", - "Multiple sequence alignment", + "Sequence clustering", + "de Novo sequencing", + "Differential gene expression analysis", + "Sequence generation", + "De-novo assembly", + "Generation", + "Genome indexing", + "Data retrieval", "Validation", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9a60ecf98d4f8134", @@ -69260,24 +84472,24 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "hmmer_jackhmmer", + "uniprotxml_downloader", + "glimmer_build-icm", + "ncbi_makeblastdb", "gffread", + "samtool_filter2", + "hmmer_jackhmmer", "samtools_fastx", - "transdecoder", "stringtie_merge", - "fasterq_dump", - "ncbi_blastp_wrapper", - "samtool_filter2", - "fastp", - "hisat2", - "ncbi_makeblastdb", - "glimmer_build-icm", "antismash", + "fastp", + "fasterq_dump", "multiqc", + "ncbi_blastp_wrapper", + "transdecoder", + "bwa_mem", "glimmer_knowlegde-based", "stringtie", - "uniprotxml_downloader" + "hisat2" ], "update_time": "2020-05-06", "versions": 7 @@ -69287,32 +84499,32 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Data handling", - "Sequence generation", - "Probabilistic sequence generation", - "Coding region prediction", - "Sequence annotation", - "De-novo assembly", - "Sequencing quality control", - "Formatting", - "Differential gene expression analysis", - "de Novo sequencing", - "Data retrieval", "Sequence contamination filtering", - "Sequence clustering", - "Genome indexing", - "Generation", + "Sequence alignment", "Database search", - "Sequence profile generation", + "Sequencing quality control", "Format validation", - "Read mapping", + "Formatting", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", "Sequence database search", - "Sequence alignment", + "Data handling", + "Sequence profile generation", + "Probabilistic sequence generation", + "Read mapping", "Gene prediction", + "Sequence clustering", "Statistical calculation", - "Multiple sequence alignment", - "Validation" + "de Novo sequencing", + "Differential gene expression analysis", + "Generation", + "Genome indexing", + "De-novo assembly", + "Sequence generation", + "Data retrieval", + "Validation", + "Sequence annotation" ], "edam_topic": [], "id": "0ab3e47ebd3b520e", @@ -69325,26 +84537,26 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "hmmer_jackhmmer", - "tophat2", - "glimmer_knowlegde-based", - "fastp", - "glimmer_build-icm", "uniprotxml_downloader", + "samtool_filter2", + "cuffquant", + "cuffmerge", + "tophat2", + "multiqc", + "fasterq_dump", + "bwa_mem", + "cuffdiff", + "ncbi_makeblastdb", "gffread", - "ncbi_blastp_wrapper", + "samtools_fastx", "antismash", + "ncbi_blastp_wrapper", "transdecoder", - "samtools_fastx", - "cuffdiff", - "cuffquant", - "ncbi_makeblastdb", - "bwa_mem", - "fasterq_dump", - "samtool_filter2", + "glimmer_knowlegde-based", + "glimmer_build-icm", "cufflinks", - "multiqc", - "cuffmerge" + "hmmer_jackhmmer", + "fastp" ], "update_time": "2020-05-06", "versions": 13 @@ -69354,9 +84566,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequencing quality control", "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", "Sequence alignment" ], "edam_topic": [], @@ -69370,11 +84582,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastq_groomer", "trimmomatic", - "rna_star", + "qualimap_rnaseq", "fastqc", - "qualimap_rnaseq" + "rna_star", + "fastq_groomer" ], "update_time": "2020-05-05", "versions": 4 @@ -69399,12 +84611,12 @@ ], "tools": [ "bio3d_pca_visualize", - "gmx_editconf", - "md_converter", "bio3d_pca", - "bio3d_rmsf", "vmd_hbonds", + "bio3d_rmsf", + "gmx_editconf", "bio3d_rmsd", + "md_converter", "mdanalysis_cosine_analysis" ], "update_time": "2020-05-04", @@ -69428,13 +84640,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ggplot2_point", - "tp_awk_tool", - "psy_maps", - "datamash_ops", "cds_essential_variability", + "climate_stripes", + "psy_maps", "Grep1", - "climate_stripes" + "ggplot2_point", + "datamash_ops", + "tp_awk_tool" ], "update_time": "2020-04-30", "versions": 0 @@ -69444,23 +84656,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Scatter plot plotting", - "Sequencing quality control", - "Pairwise sequence alignment", + "Gene prediction", + "Genome annotation", + "Visualisation", "Genome assembly", - "Box-Whisker plot plotting", + "Scatter plot plotting", "Sequence assembly visualisation", + "Mapping assembly", "Multilocus sequence typing", - "Genome visualisation", + "Sequencing quality control", + "Box-Whisker plot plotting", + "Coding region prediction", + "Pairwise sequence alignment", "Sequence assembly validation", - "Visualisation", + "Genome visualisation", + "Filtering", "Antimicrobial resistance prediction", - "Gene prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction", - "Mapping assembly" + "Taxonomic classification" ], "edam_topic": [], "id": "5826e573b6f93762", @@ -69481,21 +84693,21 @@ "long_read" ], "tools": [ - "meta_flye", - "abricate", + "prokka", + "bandage_info", "kraken2", - "Krona", - "filtlong", - "Cut1", - "bandage_image", + "racon", + "jbrowse", + "abricate", "nanoplot", + "bandage_image", + "meta_flye", "quast", - "mlst", + "Krona", + "filtlong", "minimap2", - "jbrowse", - "prokka", - "racon", - "bandage_info" + "Cut1", + "mlst" ], "update_time": "2020-04-21", "versions": 1 @@ -69538,14 +84750,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seqwish", "vg_deconstruct", "__FILTER_FAILED_DATASETS__", + "vg_convert", + "tp_cat", + "seqwish", "vg_view", - "minimap2", "minia", - "vg_convert", - "tp_cat" + "minimap2" ], "update_time": "2020-04-10", "versions": 8 @@ -69588,11 +84800,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "gops_join_1", "tp_sort_header_tool", - "tp_cut_tool", - "join1", "Grouping1", - "gops_join_1" + "join1", + "tp_cut_tool" ], "update_time": "2020-04-04", "versions": 6 @@ -69602,18 +84814,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Sequence composition calculation", + "Sequence alignment analysis", + "Generation", "Genome indexing", - "Generation" + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "40a621934a07c7ee", @@ -69626,14 +84838,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "samtools_flagstat", - "tp_sort_header_tool", "trimmomatic", - "bwa", + "deeptools_bam_coverage", "trim_galore", + "tp_sort_header_tool", "fastqc", - "bamFilter" + "bamFilter", + "bwa", + "samtools_flagstat" ], "update_time": "2020-04-03", "versions": 2 @@ -69656,13 +84868,13 @@ "cheminformatics" ], "tools": [ - "get_pdb", - "sdf_to_tab", - "tp_grep_tool", - "openbabel_compound_convert", "prepare_receptor", "prepare_box", - "docking" + "get_pdb", + "openbabel_compound_convert", + "docking", + "sdf_to_tab", + "tp_grep_tool" ], "update_time": "2020-04-02", "versions": 5 @@ -69672,9 +84884,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "c702c76cadebac30", @@ -69689,10 +84901,10 @@ "ont" ], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2020-03-29", "versions": 2 @@ -69718,9 +84930,9 @@ "ont" ], "tools": [ + "datamash_reverse", "tp_replace_in_line", "taxonomy_krona_chart", - "datamash_reverse", "kraken2" ], "update_time": "2020-03-29", @@ -69758,12 +84970,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Pairwise sequence alignment", "De-novo assembly", "Genome assembly", "Mapping assembly", - "Pairwise sequence alignment", - "Cross-assembly" + "Cross-assembly", + "Aggregation" ], "edam_topic": [], "id": "b2dfa74f55a73409", @@ -69779,9 +84991,9 @@ ], "tools": [ "minimap2", + "flye", "nanopolish_variants", - "unicycler", - "flye" + "unicycler" ], "update_time": "2020-03-29", "versions": 7 @@ -69791,20 +85003,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", "Pairwise sequence alignment", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "49ce9e738fadef4a", @@ -69819,16 +85031,16 @@ "covid-19" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "fasterq_dump", - "minimap2", "samtool_filter2", + "samtools_fastx", + "picard_MergeSamFiles", "fastp", + "fasterq_dump", + "nanoplot", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-03-29", "versions": 8 @@ -69849,11 +85061,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2020-03-27", "versions": 1 @@ -69863,8 +85075,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence annotation" + "Sequence annotation", + "Data handling" ], "edam_topic": [], "id": "799b924edd3c401b", @@ -69877,11 +85089,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "metagene_annotator", + "fastq_to_fasta_python", "regex1", - "fastq_dump", "sixgill_build", - "fastq_to_fasta_python" + "fastq_dump", + "metagene_annotator" ], "update_time": "2020-03-24", "versions": 2 @@ -69906,8 +85118,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2020-03-23", "versions": 8 @@ -69917,29 +85129,29 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", + "Sequence motif recognition", "Sequence assembly", - "Coding region prediction", + "Database search", + "Primer removal", + "Format validation", "Sequencing quality control", "Formatting", - "Data retrieval", - "Read pre-processing", + "Multiple sequence alignment", + "Coding region prediction", + "Conversion", + "Sequence database search", + "Sequence profile generation", "Sequence trimming", - "Genome assembly", - "Database search", + "Probabilistic sequence generation", "Protein feature detection", - "Sequence profile generation", - "Format validation", - "Sequence composition calculation", - "Sequence database search", "Gene prediction", - "Sequence motif recognition", - "Primer removal", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment" + "Genome assembly", + "Read pre-processing", + "Sequence generation", + "Sequence composition calculation", + "Data retrieval", + "Taxonomic classification" ], "edam_topic": [], "id": "02631612a43a4d9b", @@ -69952,22 +85164,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "interproscan", - "fasplit", + "fraggenescan", + "sort1", "collapse_dataset", - "tp_awk_tool", - "maxbin2", + "cat_bins", + "tp_cat", "trim_galore", - "tp_grep_tool", - "fraggenescan", + "fasplit", + "tp_awk_tool", "hmmer_hmmscan", - "__UNZIP_COLLECTION__", "metaspades", - "sort1", - "fastqc", "__FLATTEN__", - "cat_bins", - "tp_cat" + "fastqc", + "interproscan", + "maxbin2", + "tp_grep_tool", + "__UNZIP_COLLECTION__" ], "update_time": "2020-03-20", "versions": 27 @@ -70012,10 +85224,10 @@ "tags": [], "tools": [ "Add_a_column1", - "Cut1", + "gops_intersect_1", "Grouping1", "tp_replace_in_column", - "gops_intersect_1" + "Cut1" ], "update_time": "2020-02-25", "versions": 0 @@ -70025,19 +85237,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Variant calling", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", + "Primer removal", + "Sequencing quality control", "Sequence trimming", - "Statistical calculation", - "Sequence contamination filtering", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Primer removal", - "Nucleic acid sequence analysis", - "Validation" + "Variant calling", + "Validation", + "Mapping" ], "edam_topic": [], "id": "6514e610c79df72c", @@ -70052,44 +85264,44 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "__UNZIP_COLLECTION__", - "multiqc", + "htseq_count", + "deeptools_plot_correlation", "wig_to_bigWig", + "bctools_extract_crosslinked_nucleotides", + "bed2gff1", + "bctools_extract_alignment_ends", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", + "rna_star", + "piranha", + "Paste1", + "Filter1", + "bedtools_subtractbed", "__MERGE_COLLECTION__", - "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "bedtools_genomecoveragebed_bedgraph", - "htseq_count", - "graphprot_predict_profile", - "bctools_extract_alignment_ends", + "deeptools_multi_bam_summary", + "wc_gnu", "ngsutils_bam_filter", + "multiqc", "__SORTLIST__", - "Paste1", - "cat1", + "Extract genomic DNA 1", + "cutadapt", + "__UNZIP_COLLECTION__", "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", "deeptools_plot_fingerprint", - "rna_star", - "tp_awk_tool", - "wc_gnu", - "bed2gff1", - "deeptools_compute_gc_bias", + "bam_to_sam", + "umi_tools_extract", "bedtools_sortbed", - "piranha", - "Filter1", - "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 13 @@ -70099,17 +85311,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Nucleic acid sequence analysis", - "Validation" + "Sequence trimming", + "Validation", + "Mapping" ], "edam_topic": [], "id": "153ba1581743d31f", @@ -70124,42 +85336,42 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "__UNZIP_COLLECTION__", + "htseq_count", "wig_to_bigWig", - "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", - "__MERGE_COLLECTION__", "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "htseq_count", - "peakachu", - "bedtools_genomecoveragebed_bedgraph", + "bctools_extract_crosslinked_nucleotides", "bctools_extract_alignment_ends", - "graphprot_predict_profile", - "__SORTLIST__", - "Paste1", - "cat1", - "samtools_flagstat", - "deeptools_plot_fingerprint", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", + "fastqc", "rna_star", - "tp_awk_tool", + "Paste1", + "Filter1", + "bedtools_subtractbed", + "__MERGE_COLLECTION__", + "deeptools_multi_bam_summary", "wc_gnu", - "deeptools_compute_gc_bias", - "bedtools_sortbed", "multiqc", - "Filter1", + "__SORTLIST__", + "Extract genomic DNA 1", "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "__UNZIP_COLLECTION__", + "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", + "deeptools_plot_fingerprint", + "bam_to_sam", + "umi_tools_extract", + "bedtools_sortbed", + "peakachu", + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 18 @@ -70169,19 +85381,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Variant calling", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", + "Primer removal", + "Sequencing quality control", "Sequence trimming", - "Statistical calculation", - "Sequence contamination filtering", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Primer removal", - "Nucleic acid sequence analysis", - "Validation" + "Variant calling", + "Validation", + "Mapping" ], "edam_topic": [], "id": "24ddd188da35b061", @@ -70196,41 +85408,41 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "wig_to_bigWig", - "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "bedtools_genomecoveragebed_bedgraph", + "wig_to_bigWig", "htseq_count", - "graphprot_predict_profile", + "pureclip", + "bctools_extract_crosslinked_nucleotides", + "bed2gff1", "bctools_extract_alignment_ends", - "ngsutils_bam_filter", - "Paste1", - "cat1", - "samtools_flagstat", - "deeptools_plot_fingerprint", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", + "fastqc", "rna_star", - "tp_awk_tool", - "pureclip", + "Paste1", + "Filter1", + "bedtools_subtractbed", + "deeptools_multi_bam_summary", "wc_gnu", - "deeptools_compute_gc_bias", - "bed2gff1", - "bedtools_sortbed", + "ngsutils_bam_filter", "multiqc", - "Filter1", + "Extract genomic DNA 1", "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", + "deeptools_plot_fingerprint", + "bam_to_sam", + "umi_tools_extract", + "bedtools_sortbed", + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 17 @@ -70240,19 +85452,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Variant calling", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", + "Primer removal", + "Sequencing quality control", "Sequence trimming", - "Statistical calculation", - "Sequence contamination filtering", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Primer removal", - "Nucleic acid sequence analysis", - "Validation" + "Variant calling", + "Validation", + "Mapping" ], "edam_topic": [], "id": "b619339f4e1c6fdf", @@ -70267,44 +85479,44 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "__UNZIP_COLLECTION__", - "multiqc", + "htseq_count", + "deeptools_plot_correlation", "wig_to_bigWig", + "bctools_extract_crosslinked_nucleotides", + "bed2gff1", + "bctools_extract_alignment_ends", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", + "rna_star", + "piranha", + "Paste1", + "Filter1", + "bedtools_subtractbed", "__MERGE_COLLECTION__", - "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "bedtools_genomecoveragebed_bedgraph", - "htseq_count", - "graphprot_predict_profile", - "bctools_extract_alignment_ends", + "deeptools_multi_bam_summary", + "wc_gnu", "ngsutils_bam_filter", + "multiqc", "__SORTLIST__", - "Paste1", - "cat1", + "Extract genomic DNA 1", + "cutadapt", + "__UNZIP_COLLECTION__", "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", "deeptools_plot_fingerprint", - "rna_star", - "tp_awk_tool", - "wc_gnu", - "bed2gff1", - "deeptools_compute_gc_bias", + "bam_to_sam", + "umi_tools_extract", "bedtools_sortbed", - "piranha", - "Filter1", - "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 14 @@ -70314,19 +85526,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Variant calling", + "Sequence contamination filtering", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", + "Primer removal", + "Sequencing quality control", "Sequence trimming", - "Statistical calculation", - "Sequence contamination filtering", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Primer removal", - "Nucleic acid sequence analysis", - "Validation" + "Variant calling", + "Validation", + "Mapping" ], "edam_topic": [], "id": "8fb156020285e049", @@ -70341,41 +85553,41 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "wig_to_bigWig", - "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "bedtools_genomecoveragebed_bedgraph", + "wig_to_bigWig", "htseq_count", - "graphprot_predict_profile", + "pureclip", + "bctools_extract_crosslinked_nucleotides", + "bed2gff1", "bctools_extract_alignment_ends", - "ngsutils_bam_filter", - "Paste1", - "cat1", - "samtools_flagstat", - "deeptools_plot_fingerprint", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", + "fastqc", "rna_star", - "tp_awk_tool", - "pureclip", + "Paste1", + "Filter1", + "bedtools_subtractbed", + "deeptools_multi_bam_summary", "wc_gnu", - "deeptools_compute_gc_bias", - "bed2gff1", - "bedtools_sortbed", + "ngsutils_bam_filter", "multiqc", - "Filter1", + "Extract genomic DNA 1", "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", + "deeptools_plot_fingerprint", + "bam_to_sam", + "umi_tools_extract", + "bedtools_sortbed", + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 22 @@ -70385,17 +85597,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Nucleic acid sequence analysis", - "Validation" + "Sequence trimming", + "Validation", + "Mapping" ], "edam_topic": [], "id": "0c619b25c1394a09", @@ -70410,42 +85622,42 @@ "clip-explorer" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "bedtools_subtractbed", - "__UNZIP_COLLECTION__", + "htseq_count", "wig_to_bigWig", - "fastqc", - "umi_tools_extract", - "bam_to_sam", - "Extract genomic DNA 1", - "__MERGE_COLLECTION__", "deeptools_plot_correlation", - "meme_chip", - "sam_to_bam", - "rcas", - "bedtools_intersectbed", - "htseq_count", - "peakachu", - "bedtools_genomecoveragebed_bedgraph", + "bctools_extract_crosslinked_nucleotides", "bctools_extract_alignment_ends", - "graphprot_predict_profile", - "__SORTLIST__", - "Paste1", - "cat1", - "samtools_flagstat", - "deeptools_plot_fingerprint", + "rcas", + "deeptools_compute_gc_bias", + "sam_to_bam", + "fastqc", "rna_star", - "tp_awk_tool", + "Paste1", + "Filter1", + "bedtools_subtractbed", + "__MERGE_COLLECTION__", + "deeptools_multi_bam_summary", "wc_gnu", - "deeptools_compute_gc_bias", - "bedtools_sortbed", "multiqc", - "Filter1", + "__SORTLIST__", + "Extract genomic DNA 1", "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "__UNZIP_COLLECTION__", + "samtools_flagstat", + "cat1", + "bedtools_genomecoveragebed_bedgraph", + "meme_chip", + "deeptools_plot_fingerprint", + "bam_to_sam", + "umi_tools_extract", + "bedtools_sortbed", + "peakachu", + "bedtools_slopbed", + "picard_CollectInsertSizeMetrics", + "bedtools_intersectbed", + "umi_tools_dedup", + "graphprot_predict_profile", + "tp_awk_tool" ], "update_time": "2020-02-24", "versions": 15 @@ -70455,19 +85667,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", - "Pairwise sequence alignment", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", + "Pairwise sequence alignment", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "dd3193aaaf08e798", @@ -70482,15 +85694,15 @@ "covid-19" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "minimap2", "samtool_filter2", - "fastp", + "samtools_fastx", + "picard_MergeSamFiles", "multiqc", - "fastqc" + "fastp", + "nanoplot", + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-02-23", "versions": 1 @@ -70500,12 +85712,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "402b14906a03b2ef", @@ -70520,8 +85732,8 @@ "covid-19" ], "tools": [ - "EMBOSS: transeq101", "rbc_mafft", + "EMBOSS: transeq101", "EMBOSS: tranalign100" ], "update_time": "2020-02-21", @@ -70532,15 +85744,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Statistical calculation", "Sequence alignment", "Phylogenetic tree generation (from molecular sequences)", - "Statistical calculation", - "Global alignment", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "e7f03b4bd9b3d6fd", @@ -70555,12 +85767,12 @@ "covid-19" ], "tools": [ + "rbc_mafft", + "EMBOSS: transeq101", "fasttree", "hyphy_gard", - "EMBOSS: transeq101", - "rbc_mafft", - "hyphy_absrel", - "EMBOSS: tranalign100" + "EMBOSS: tranalign100", + "hyphy_absrel" ], "update_time": "2020-02-21", "versions": 2 @@ -70570,10 +85782,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment", "Formatting", - "Phylogenetic tree generation (from molecular sequences)" + "Multiple sequence alignment" ], "edam_topic": [], "id": "9155ed0e7a6a7b60", @@ -70588,15 +85800,15 @@ "covid-19" ], "tools": [ - "fasttree", - "ncbi_acc_download", - "collapse_dataset", "picard_NormalizeFasta", - "Cut1", - "tp_sed_tool", "rbc_mafft", + "fasttree", + "collapse_dataset", "Remove beginning1", - "Convert characters1" + "Convert characters1", + "tp_sed_tool", + "ncbi_acc_download", + "Cut1" ], "update_time": "2020-02-21", "versions": 2 @@ -70606,9 +85818,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "7b755497d168cb13", @@ -70623,10 +85835,10 @@ "covid-19" ], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2020-02-21", "versions": 2 @@ -70649,10 +85861,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_tail_tool", - "tab2fasta", "ncbi_makeblastdb", + "tab2fasta", "ncbi_blastn_wrapper", + "tp_tail_tool", "clustalw" ], "update_time": "2020-02-19", @@ -70674,17 +85886,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gmx_makendx", + "gmx_solvate", + "gmx_setup", "ambertools_acpype", - "gmx_editconf", "get_pdb", - "gmx_solvate", - "tp_grep_tool", - "gmx_sim", - "gmx_restraints", "openbabel_compound_convert", "gmx_em", - "gmx_setup" + "gmx_makendx", + "gmx_restraints", + "gmx_editconf", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2020-02-14", "versions": 1 @@ -70695,9 +85907,9 @@ "doi": "", "edam_operation": [ "Read mapping", - "RNA-Seq analysis", "Nucleic acid sequence analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "5b46c8533cd95447", @@ -70711,10 +85923,10 @@ "tags": [], "tools": [ "htseq_count", - "sort1", + "bowtie2", "Filter1", - "deseq2", - "bowtie2" + "sort1", + "deseq2" ], "update_time": "2020-02-13", "versions": 2 @@ -70724,25 +85936,25 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", + "Genome annotation", "Visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", "Mapping assembly", + "Sequencing quality control", "Cross-assembly", - "Filtering", + "Box-Whisker plot plotting", + "Coding region prediction", + "Sequence assembly validation", + "Gene prediction", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Multilocus sequence typing", + "Pairwise sequence alignment", + "De-novo assembly", "Genome visualisation", - "Sequence assembly validation", - "Gene prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction" + "Filtering", + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "a337bfb2eb1e583f", @@ -70759,21 +85971,21 @@ "ont" ], "tools": [ - "abricate", + "prokka", "flye", + "bandage_info", "kraken2", - "filtlong", - "Cut1", - "bandage_image", + "racon", + "jbrowse", + "abricate", + "taxonomy_krona_chart", "nanoplot", + "bandage_image", "quast", - "mlst", + "filtlong", "minimap2", - "taxonomy_krona_chart", - "jbrowse", - "prokka", - "racon", - "bandage_info" + "Cut1", + "mlst" ], "update_time": "2020-02-10", "versions": 4 @@ -70783,25 +85995,25 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", + "Genome annotation", "Visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", "Mapping assembly", + "Sequencing quality control", "Cross-assembly", - "Filtering", + "Box-Whisker plot plotting", + "Coding region prediction", + "Sequence assembly validation", + "Gene prediction", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Multilocus sequence typing", + "Pairwise sequence alignment", + "De-novo assembly", "Genome visualisation", - "Sequence assembly validation", - "Gene prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction" + "Filtering", + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "a84bac86ec183d46", @@ -70818,21 +86030,21 @@ "ont" ], "tools": [ - "abricate", + "prokka", "flye", + "bandage_info", "kraken2", - "filtlong", - "Cut1", - "bandage_image", + "racon", + "jbrowse", + "abricate", + "taxonomy_krona_chart", "nanoplot", + "bandage_image", "quast", - "mlst", + "filtlong", "minimap2", - "taxonomy_krona_chart", - "jbrowse", - "prokka", - "racon", - "bandage_info" + "Cut1", + "mlst" ], "update_time": "2020-02-10", "versions": 8 @@ -70855,12 +86067,12 @@ "ml" ], "tools": [ + "sklearn_searchcv", + "plotly_regression_performance_plots", + "sklearn_generalized_linear", "sklearn_build_pipeline", "sklearn_ensemble", - "sklearn_generalized_linear", - "Remove beginning1", - "sklearn_searchcv", - "plotly_regression_performance_plots" + "Remove beginning1" ], "update_time": "2020-01-24", "versions": 2 @@ -70881,11 +86093,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2020-01-22", "versions": 3 @@ -70906,11 +86118,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2020-01-15", "versions": 2 @@ -70931,11 +86143,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2020-01-15", "versions": 1 @@ -70956,11 +86168,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2020-01-15", "versions": 4 @@ -71006,10 +86218,10 @@ "ml" ], "tools": [ - "sklearn_build_pipeline", "sklearn_searchcv", - "sklearn_ensemble", - "plotly_regression_performance_plots" + "plotly_regression_performance_plots", + "sklearn_build_pipeline", + "sklearn_ensemble" ], "update_time": "2020-01-10", "versions": 1 @@ -71033,8 +86245,8 @@ ], "tools": [ "plotly_parallel_coordinates_plot", - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-01-10", "versions": 1 @@ -71104,8 +86316,8 @@ "ml" ], "tools": [ - "sklearn_ensemble", - "plotly_regression_performance_plots" + "plotly_regression_performance_plots", + "sklearn_ensemble" ], "update_time": "2020-01-09", "versions": 2 @@ -71126,19 +86338,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "scanpy_compute_graph", "scanpy_read_10x", - "scanpy_parameter_iterator", - "_ensembl_gtf2gene_list", "scanpy_run_tsne", + "scanpy_find_cluster", + "_ensembl_gtf2gene_list", + "scanpy_parameter_iterator", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2020-01-09", "versions": 4 @@ -71159,20 +86371,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ucsc_cell_browser", - "seurat_find_variable_genes", "seurat_scale_data", - "seurat_run_tsne", - "seurat_normalise_data", - "seurat_find_markers", - "seurat_export_cellbrowser", + "retrieve_scxa", "seurat_run_pca", + "seurat_normalise_data", "seurat_find_clusters", + "seurat_create_seurat_object", + "seurat_find_markers", "seurat_filter_cells", + "seurat_run_tsne", + "ucsc_cell_browser", + "seurat_find_variable_genes", + "seurat_dim_plot", "seurat_read10x", - "seurat_create_seurat_object", - "retrieve_scxa", - "seurat_dim_plot" + "seurat_export_cellbrowser" ], "update_time": "2020-01-09", "versions": 2 @@ -71196,14 +86408,14 @@ ], "tools": [ "ctb_simsearch", - "ctb_chemfp_mol2fps", + "Show beginning1", + "tp_cat", + "Remove beginning1", + "comp1", "ctb_chemfp_butina_clustering", "tp_cut_tool", - "tp_grep_tool", - "comp1", - "Remove beginning1", - "Show beginning1", - "tp_cat" + "ctb_chemfp_mol2fps", + "tp_grep_tool" ], "update_time": "2020-01-09", "versions": 5 @@ -71227,19 +86439,19 @@ "ml" ], "tools": [ - "tp_easyjoin_tool", - "ctb_mordred_descriptors", - "Cut1", - "openbabel_remDuplicates", - "tp_sorted_uniq", - "tp_grep_tool", + "Paste1", + "openbabel_remIons", "sklearn_ensemble", - "sklearn_train_test_split", - "Remove beginning1", "plotly_ml_performance_plots", - "openbabel_remIons", + "tp_grep_tool", + "openbabel_remDuplicates", + "Remove beginning1", + "tp_easyjoin_tool", "tp_replace_in_column", - "Paste1" + "ctb_mordred_descriptors", + "tp_sorted_uniq", + "Cut1", + "sklearn_train_test_split" ], "update_time": "2020-01-09", "versions": 5 @@ -71285,20 +86497,20 @@ "cheminformatics" ], "tools": [ - "ctb_online_data_fetch", "cat1", + "Filter1", "sed_stream_editor", "openbabel_remIons", - "Cut1", - "tp_grep_tool", + "ctb_online_data_fetch", "ctb_pubchem_download_as_smiles", "mergeCols1", - "addValue", + "Cut1", + "Grep1", "Convert characters1", - "bg_uniq", "openbabel_compound_convert", - "Filter1", - "Grep1" + "tp_grep_tool", + "addValue", + "bg_uniq" ], "update_time": "2019-12-20", "versions": 3 @@ -71321,14 +86533,14 @@ "cheminformatics" ], "tools": [ - "chembl", - "get_pdb", - "sdf_to_tab", - "tp_grep_tool", - "openbabel_compound_convert", "prepare_receptor", "prepare_box", - "docking" + "get_pdb", + "openbabel_compound_convert", + "docking", + "sdf_to_tab", + "chembl", + "tp_grep_tool" ], "update_time": "2019-12-20", "versions": 2 @@ -71351,20 +86563,20 @@ "cheminformatics" ], "tools": [ - "chembl", - "ctb_chemfp_mol2fps", - "ctb_chemfp_butina_clustering", + "prepare_receptor", "collapse_dataset", - "get_pdb", - "sdf_to_tab", - "tp_grep_tool", + "prepare_box", + "tp_cat", "ctb_chemfp_nxn_clustering", - "addValue", + "get_pdb", "openbabel_compound_convert", - "prepare_receptor", - "prepare_box", "docking", - "tp_cat" + "sdf_to_tab", + "ctb_chemfp_butina_clustering", + "ctb_chemfp_mol2fps", + "chembl", + "tp_grep_tool", + "addValue" ], "update_time": "2019-12-20", "versions": 2 @@ -71387,9 +86599,9 @@ "proteogenomics" ], "tools": [ - "pep_pointer", + "peptide_genomic_coordinate", "query_tabular", - "peptide_genomic_coordinate" + "pep_pointer" ], "update_time": "2019-12-17", "versions": 3 @@ -71399,8 +86611,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "edea08c943ff9c5e", @@ -71415,16 +86627,16 @@ "proteogenomics" ], "tools": [ - "fasta2tab", - "search_gui", - "peptide_shaker", - "Cut1", + "query_tabular", "tab2fasta", "ncbi_blastp_wrapper", + "fasta2tab", + "search_gui", "Convert characters1", "Grouping1", "mz_to_sqlite", - "query_tabular" + "Cut1", + "peptide_shaker" ], "update_time": "2019-12-17", "versions": 6 @@ -71434,12 +86646,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "a2f36d4dd48d8ec2", @@ -71454,21 +86666,21 @@ "proteogenomics" ], "tools": [ - "gffcompare", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "translate_bed", - "tp_replace_in_line", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", "sqlite_to_tabular", + "tp_replace_in_line", + "tp_cat", "stringtie", + "translate_bed", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "gffcompare", + "hisat2", + "bed_to_protein_map" ], "update_time": "2019-12-17", "versions": 17 @@ -71478,16 +86690,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Multilocus sequence typing", "Gene prediction", - "Antimicrobial resistance prediction", "Genome annotation", "Statistical calculation", "Genome assembly", + "Multilocus sequence typing", + "Sequencing quality control", "Coding region prediction", - "Validation" + "Sequence composition calculation", + "Validation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "42c0da2e86318b37", @@ -71500,14 +86712,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "abricate", + "prokka", "trimmomatic", - "mlst", + "abricate", "multiqc", - "shovill", - "prokka", + "__FLATTEN__", "fastqc", - "__FLATTEN__" + "mlst", + "shovill" ], "update_time": "2019-12-12", "versions": 15 @@ -71517,14 +86729,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", "Sequence alignment", + "Differential gene expression analysis", "Validation", - "Differential gene expression analysis" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0fa523529c4f73cf", @@ -71537,10 +86749,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", "htseq_count", "multiqc", "fastqc", + "rna_star", "deseq2" ], "update_time": "2019-12-10", @@ -71576,16 +86788,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Generation", - "RNA-Seq quantification" + "Genome indexing", + "RNA-Seq quantification", + "Read summarisation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "b86f3775aa1f13bc", @@ -71599,17 +86811,17 @@ "tags": [], "tools": [ "bg_find_subsequences", - "deeptools_bam_coverage", "Add_a_column1", - "tp_easyjoin_tool", - "tp_sort_header_tool", + "featurecounts", "trimmomatic", "Cut1", - "bwa", - "fastq_dump", + "deeptools_bam_coverage", "fasterq_dump", - "featurecounts", - "fastqc" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "fastqc", + "bwa", + "fastq_dump" ], "update_time": "2019-12-02", "versions": 0 @@ -71632,20 +86844,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "anndata_inspect", + "anndata_import", "scanpy_plot", + "tp_tail_tool", "anndata_manipulate", - "anndata_import", - "tp_awk_tool", "Cut1", - "scanpy_filter", "scanpy_inspect", - "scanpy_normalize", - "scanpy_cluster_reduce_dimension", "tp_cat", + "scanpy_normalize", "scanpy_remove_confounders", "tp_replace_in_column", - "tp_tail_tool" + "scanpy_cluster_reduce_dimension", + "scanpy_filter", + "anndata_inspect", + "tp_awk_tool" ], "update_time": "2019-11-25", "versions": 1 @@ -71655,17 +86867,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Ab-initio gene prediction", - "Genome visualisation", - "Sequence assembly validation", - "Genome annotation", "Gene prediction", + "Genome annotation", "Homology-based gene prediction", - "Scaffolding", "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Operation", - "Transcriptome assembly" + "Sequence assembly validation", + "Ab-initio gene prediction", + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "6ca20e710f4f3ffb", @@ -71680,12 +86892,12 @@ "tools": [ "jcvi_gff_stats", "gffread", - "maker", - "augustus_training", "fasta-stats", - "jbrowse", + "snap_training", "busco", - "snap_training" + "maker", + "jbrowse", + "augustus_training" ], "update_time": "2019-11-01", "versions": 0 @@ -71794,18 +87006,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "split_file_to_collection", "search_gui", - "peptide_shaker", - "filter_by_fasta_ids", "tp_sort_header_tool", - "Cut1", - "addValue", - "query_tabular", + "filter_by_fasta_ids", + "tp_easyjoin_tool", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "split_file_to_collection" + "addValue", + "peptide_shaker" ], "update_time": "2019-10-24", "versions": 2 @@ -71826,18 +87038,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "split_file_to_collection", "search_gui", - "peptide_shaker", - "filter_by_fasta_ids", "tp_sort_header_tool", - "Cut1", - "addValue", - "query_tabular", + "filter_by_fasta_ids", + "tp_easyjoin_tool", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "split_file_to_collection" + "addValue", + "peptide_shaker" ], "update_time": "2019-10-24", "versions": 18 @@ -71847,14 +87059,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Aggregation", - "Primer removal", "Read pre-processing", + "Sequence assembly visualisation", + "Genome assembly", "Sequence trimming", + "Primer removal", "Sequencing quality control", - "Genome assembly", - "Sequence assembly visualisation" + "Filtering", + "Aggregation" ], "edam_topic": [], "id": "346b46e6316c6950", @@ -71870,10 +87082,10 @@ ], "tools": [ "porechop", - "filtlong", "bandage_image", "trim_galore", - "unicycler" + "unicycler", + "filtlong" ], "update_time": "2019-10-23", "versions": 1 @@ -71883,14 +87095,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Mapping assembly", + "Pairwise sequence alignment", "De-novo assembly", - "Genome assembly", + "Sequence assembly visualisation", "Sequence analysis", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation" + "Genome assembly", + "Scatter plot plotting", + "Mapping assembly", + "Box-Whisker plot plotting" ], "edam_topic": [], "id": "32d2f5340098bcbd", @@ -71905,14 +87117,14 @@ "ont" ], "tools": [ + "miniasm", + "racon", + "PlasFlow", "gfa_to_fa", - "bandage_image", "nanoplot", - "staramr_search", + "bandage_image", "minimap2", - "PlasFlow", - "miniasm", - "racon" + "staramr_search" ], "update_time": "2019-10-22", "versions": 1 @@ -71923,12 +87135,12 @@ "doi": "", "edam_operation": [ "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Sequence composition calculation", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", - "Sequence alignment" + "Genome indexing", + "Read mapping" ], "edam_topic": [], "id": "11290f22e13899bd", @@ -71941,11 +87153,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "deeptools_bam_coverage", - "bwa", + "bam_to_sam", "fastqc", - "bowtie2", - "bam_to_sam" + "bwa" ], "update_time": "2019-10-18", "versions": 0 @@ -71955,14 +87167,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "fba10ba449498bb5", @@ -71975,10 +87187,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", + "freebayes", "trimmomatic", "vcffilter2", - "freebayes", + "bwa_mem", "fastqc" ], "update_time": "2019-10-18", @@ -72062,13 +87274,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Differential gene expression analysis", + "RNA-Seq analysis", "Sequence alignment", + "Differential gene expression analysis", + "RNA-Seq quantification", "Read summarisation", - "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence annotation", + "Transcriptome assembly" ], "edam_topic": [], "id": "2287afbf248d9c89", @@ -72081,17 +87293,17 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "gffcompare", - "trimmomatic", - "stringtie_merge", - "featurecounts", "Filter1", "sort1", - "hisat2", - "deseq2", + "featurecounts", + "trimmomatic", + "stringtie_merge", + "deeptools_bam_coverage", + "Grep1", + "gffcompare", "stringtie", - "Grep1" + "hisat2", + "deseq2" ], "update_time": "2019-10-07", "versions": 0 @@ -72102,12 +87314,12 @@ "doi": "", "edam_operation": [ "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Sequence composition calculation", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", - "Sequence alignment" + "Genome indexing", + "Read mapping" ], "edam_topic": [], "id": "da5d4e3e6c66cf3b", @@ -72120,11 +87332,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bowtie2", "deeptools_bam_coverage", - "bwa", + "bam_to_sam", "fastqc", - "bowtie2", - "bam_to_sam" + "bwa" ], "update_time": "2019-10-04", "versions": 0 @@ -72156,15 +87368,15 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", + "Genome assembly", + "Sequencing quality control", + "Formatting", "Aggregation", "De-novo assembly", "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence assembly validation", - "Visualisation", - "Statistical calculation", - "Genome assembly" + "Sequence assembly validation" ], "edam_topic": [], "id": "842e0ea7b1eb56af", @@ -72177,12 +87389,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "unicycler", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "fastqc", - "unicycler" + "fastqc" ], "update_time": "2019-09-27", "versions": 0 @@ -72205,20 +87417,20 @@ "ips" ], "tools": [ - "MSGFPlusAdapter", - "IDFilter", + "FileMerger", "FeatureFinderMultiplex", "FalseDiscoveryRate", - "IDConflictResolver", - "MultiplexResolver", "PeptideIndexer", - "MzTabExporter", + "HighResPrecursorMassCorrector", + "IDFilter", + "IDConflictResolver", "ConsensusID", "IDMapper", - "FileMerger", + "MSGFPlusAdapter", + "IDMerger", "FileFilter", - "HighResPrecursorMassCorrector", - "IDMerger" + "MultiplexResolver", + "MzTabExporter" ], "update_time": "2019-09-25", "versions": 4 @@ -72242,9 +87454,9 @@ "meinbio" ], "tools": [ - "tp_awk_tool", + "tp_sed_tool", "table_compute", - "tp_sed_tool" + "tp_awk_tool" ], "update_time": "2019-09-23", "versions": 1 @@ -72267,15 +87479,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "regionalgam_plot_trend", "regionalgam_flight_curve", - "ggplot2_point", - "tp_awk_tool", + "regionalgam_gls", + "regionalgam_glmmpql", "Count1", "regionalgam_autocor_acf", + "ggplot2_point", "regionalgam_ab_index", - "regionalgam_glmmpql", - "regionalgam_gls" + "tp_awk_tool", + "regionalgam_plot_trend" ], "update_time": "2019-09-23", "versions": 2 @@ -72285,10 +87497,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Genetic variation analysis", + "Statistical calculation", "Sequence analysis", - "Variant calling", - "Statistical calculation" + "Genetic variation analysis", + "Variant calling" ], "edam_topic": [], "id": "3570835f21365be7", @@ -72304,12 +87516,12 @@ "training-material" ], "tools": [ - "bcftools_norm", - "gemini_load", - "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "samtools_rmdup", "samtool_filter2", + "bcftools_norm", + "gemini_load", "gemini_inheritance" ], "update_time": "2019-09-21", @@ -72320,17 +87532,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", - "Genetic variation analysis", - "Sequence analysis", "Statistical calculation", - "Genome indexing", + "Genetic variation analysis", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Sequence analysis", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "2aede5c6577b28f5", @@ -72346,15 +87558,15 @@ "training-material" ], "tools": [ - "bcftools_norm", - "bwa_mem", - "gemini_load", "samtools_rmdup", - "snpEff", - "freebayes", "samtool_filter2", + "freebayes", + "bcftools_norm", + "snpEff", + "gemini_load", "multiqc", "gemini_inheritance", + "bwa_mem", "fastqc" ], "update_time": "2019-09-21", @@ -72376,10 +87588,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sklearn_estimator_attributes", - "sklearn_build_pipeline", "plotly_parallel_coordinates_plot", - "sklearn_searchcv" + "sklearn_estimator_attributes", + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2019-09-16", "versions": 1 @@ -72389,13 +87601,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "Sequencing quality control", - "Sequence alignment", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "49073a24429d93d6", @@ -72408,14 +87620,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", - "featurecounts", - "tp_sed_tool", - "umi_tools_count", "samtools_stats", + "featurecounts", "multiqc", + "bamFilter", "umi_tools_extract", - "bamFilter" + "tp_sed_tool", + "rna_star", + "umi_tools_count" ], "update_time": "2019-09-04", "versions": 5 @@ -72472,16 +87684,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", + "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", "Primer removal", + "Phylogenetic analysis", "Read pre-processing", - "Sequence clustering", - "Sequence read processing", "Sequence trimming", - "DNA barcoding" + "Sequence read processing", + "Taxonomic classification" ], "edam_topic": [], "id": "b91a380ceaa0342b", @@ -72494,27 +87706,27 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "trim_galore", - "mothur_count_seqs", - "mothur_classify_otu", - "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", - "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_count_groups", "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_unique_seqs", + "mothur_classify_otu", "mothur_summary_seqs", "mothur_align_seqs", - "mothur_remove_lineage", + "taxonomy_krona_chart", + "trim_galore", + "mothur_filter_seqs", "mothur_remove_seqs", - "mothur_unique_seqs" + "mothur_summary_single", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", + "mothur_pre_cluster", + "mothur_chimera_vsearch", + "mothur_make_contigs" ], "update_time": "2019-08-07", "versions": 0 @@ -72524,16 +87736,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", + "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", "Primer removal", + "Phylogenetic analysis", "Read pre-processing", - "Sequence clustering", - "Sequence read processing", "Sequence trimming", - "DNA barcoding" + "Sequence read processing", + "Taxonomic classification" ], "edam_topic": [], "id": "b66e1d8171e6dac2", @@ -72546,27 +87758,27 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "trim_galore", - "mothur_count_seqs", - "mothur_classify_otu", - "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", - "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_count_groups", "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_unique_seqs", + "mothur_classify_otu", "mothur_summary_seqs", "mothur_align_seqs", - "mothur_remove_lineage", + "taxonomy_krona_chart", + "trim_galore", + "mothur_filter_seqs", "mothur_remove_seqs", - "mothur_unique_seqs" + "mothur_summary_single", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", + "mothur_pre_cluster", + "mothur_chimera_vsearch", + "mothur_make_contigs" ], "update_time": "2019-08-05", "versions": 2 @@ -72587,8 +87799,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "vigiechiro_idcorrect_2ndlayer", "vigiechiro_idvalid", + "vigiechiro_idcorrect_2ndlayer", "vigiechiro_bilanenrichipf" ], "update_time": "2019-07-31", @@ -72610,8 +87822,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "vigiechiro_idcorrect_2ndlayer", "vigiechiro_idvalid", + "vigiechiro_idcorrect_2ndlayer", "vigiechiro_bilanenrichirp" ], "update_time": "2019-07-31", @@ -72622,16 +87834,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Mapping", + "Statistical calculation", "Sequencing quality control", + "Sequence composition calculation", "Gene regulatory network analysis", - "Statistical calculation", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "6bce1d419a179c50", @@ -72644,25 +87856,25 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "fastqc", - "deeptools_compute_matrix", - "Extract genomic DNA 1", - "deeptools_multi_bigwig_summary", "deeptools_plot_correlation", - "macs2_callpeak", - "deeptools_plot_pca", - "deeptools_bigwig_compare", + "bed2gff1", "chipseeker", + "trimmomatic", "deeptools_bam_coverage", + "deeptools_bigwig_compare", + "fastqc", + "resize_coordinate_window", + "bowtie2", + "multiqc", "deeptools_plot_heatmap", - "trimmomatic", + "deeptools_compute_matrix", + "Extract genomic DNA 1", + "deeptools_plot_pca", + "macs2_callpeak", "deeptools_plot_fingerprint", - "bed2gff1", "fastq_dump", - "resize_coordinate_window", - "multiqc", - "bowtie2", - "bedtools_intersectbed" + "bedtools_intersectbed", + "deeptools_multi_bigwig_summary" ], "update_time": "2019-07-30", "versions": 1 @@ -72686,9 +87898,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "datamash_reverse", "tp_replace_in_line", "taxonomy_krona_chart", - "datamash_reverse", "kraken2" ], "update_time": "2019-07-22", @@ -72710,20 +87922,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ucsc_cell_browser", - "retrieve_scxa", - "scanpy_compute_graph", "scanpy_read_10x", "scanpy_run_tsne", + "retrieve_scxa", + "scanpy_find_cluster", "scanpy_find_markers", - "scanpy_run_pca", "scanpy_run_umap", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", + "ucsc_cell_browser", "scanpy_scale_data", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "scanpy_normalise_data", + "scanpy_compute_graph" ], "update_time": "2019-07-10", "versions": 3 @@ -72733,9 +87945,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", "Coding region prediction", + "Genome visualisation", "Genome annotation" ], "edam_topic": [], @@ -72749,8 +87961,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2019-07-02", "versions": 0 @@ -72795,11 +88007,11 @@ "gcc2019" ], "tools": [ - "IDScoreSwitcher", "FalseDiscoveryRate", + "IDPosteriorErrorProbability", "PeptideIndexer", "FileInfo", - "IDPosteriorErrorProbability" + "IDScoreSwitcher" ], "update_time": "2019-06-30", "versions": 3 @@ -72809,14 +88021,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "9e0d784860d6cc91", @@ -72829,19 +88041,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Paste1", "cat1", + "Filter1", "Add_a_column1", "datamash_transpose", + "histogram_rpy", "wc_gnu", - "Cut1", - "Summary_Statistics1", "ggplot2_histogram", + "Cut1", + "venn_list", "Remove beginning1", + "Summary_Statistics1", "dbbuilder", - "Filter1", - "venn_list", - "histogram_rpy", - "Paste1", "maxquant" ], "update_time": "2019-06-29", @@ -72864,8 +88076,8 @@ "tags": [], "tools": [ "tp_head_tool", - "__FILTER_FROM_FILE__", - "tp_grep_tool" + "tp_grep_tool", + "__FILTER_FROM_FILE__" ], "update_time": "2019-06-28", "versions": 5 @@ -72875,13 +88087,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -72895,13 +88107,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "datamash_ops", - "velvetg", - "multiqc", - "fastqc" + "fastqc", + "datamash_ops" ], "update_time": "2019-06-27", "versions": 4 @@ -72912,11 +88124,11 @@ "doi": "", "edam_operation": [ "De-novo assembly", - "Sequence assembly", "Genome assembly", + "Sequence assembly visualisation", "Optimisation and refinement", - "Formatting", - "Sequence assembly visualisation" + "Sequence assembly", + "Formatting" ], "edam_topic": [], "id": "ef83f7fd2176a244", @@ -72929,12 +88141,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "velveth", - "bandage_image", "fasta-stats", + "spades", + "bandage_image", "velvetg", - "velvetoptimiser", - "spades" + "velveth", + "velvetoptimiser" ], "update_time": "2019-06-27", "versions": 5 @@ -72944,19 +88156,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Formatting", - "Sequence comparison", "Visualisation", - "Phylogenetic inference", "Primer removal", + "Sequence comparison", + "Phylogenetic tree editing", + "Formatting", + "Sequence similarity search", "Read pre-processing", - "Taxonomic classification", - "Phylogenetic tree visualisation", + "Conversion", + "Sequence alignment analysis", + "Phylogenetic inference", "Sequence trimming", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "7ab70660e6235cf0", @@ -72971,21 +88183,21 @@ "gcc2019" ], "tools": [ - "bg_sortmerna", - "group_humann2_uniref_abundances_to_go", - "fastq_groomer", - "metaphlan2krona", - "metaphlan2", + "export2graphlan", "graphlan_annotate", + "bg_sortmerna", "combine_metaphlan2_humann2", - "graphlan", + "taxonomy_krona_chart", + "metaphlan2", "fastq_paired_end_interlacer", - "format_metaphlan2_output", + "group_humann2_uniref_abundances_to_go", "humann2_genefamilies_genus_level", - "taxonomy_krona_chart", + "metaphlan2krona", + "graphlan", "humann2", "cutadapt", - "export2graphlan" + "format_metaphlan2_output", + "fastq_groomer" ], "update_time": "2019-06-26", "versions": 5 @@ -72995,19 +88207,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Formatting", - "Sequence comparison", "Visualisation", - "Phylogenetic inference", "Primer removal", + "Sequence comparison", + "Phylogenetic tree editing", + "Formatting", + "Sequence similarity search", "Read pre-processing", - "Taxonomic classification", - "Phylogenetic tree visualisation", + "Conversion", + "Sequence alignment analysis", + "Phylogenetic inference", "Sequence trimming", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "994e5ff1df7d6c9e", @@ -73022,17 +88234,17 @@ "gcc2019" ], "tools": [ + "export2graphlan", + "graphlan_annotate", "bg_sortmerna", - "fastq_groomer", - "metaphlan2krona", + "taxonomy_krona_chart", "metaphlan2", - "graphlan_annotate", - "graphlan", "fastq_paired_end_interlacer", - "format_metaphlan2_output", - "taxonomy_krona_chart", + "graphlan", + "metaphlan2krona", "cutadapt", - "export2graphlan" + "format_metaphlan2_output", + "fastq_groomer" ], "update_time": "2019-06-26", "versions": 2 @@ -73055,9 +88267,9 @@ "gcc2019" ], "tools": [ + "humann2_genefamilies_genus_level", "combine_metaphlan2_humann2", - "group_humann2_uniref_abundances_to_go", - "humann2_genefamilies_genus_level" + "group_humann2_uniref_abundances_to_go" ], "update_time": "2019-06-26", "versions": 3 @@ -73083,10 +88295,10 @@ "name:mapvisualization" ], "tools": [ - "Count1", - "Summary_Statistics1", "spocc_occ", "Filter1", + "Summary_Statistics1", + "Count1", "gdal_ogr2ogr" ], "update_time": "2019-06-22", @@ -73149,13 +88361,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "Sequencing quality control", - "Sequence alignment", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "f841e1207611f28f", @@ -73168,12 +88380,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", "featurecounts", - "umi_tools_count", "multiqc", + "bamFilter", "umi_tools_extract", - "bamFilter" + "rna_star", + "umi_tools_count" ], "update_time": "2019-05-22", "versions": 3 @@ -73207,12 +88419,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "De-novo assembly", - "Sequencing quality control", "Pairwise sequence alignment", + "De-novo assembly", "Genome assembly", "Mapping assembly", + "Sequencing quality control", + "Filtering", "Cross-assembly" ], "edam_topic": [], @@ -73230,11 +88442,11 @@ ], "tools": [ "flye", + "racon", + "bam_to_sam", "filtlong", "minimap2", - "nanopolish_variants", - "racon", - "bam_to_sam" + "nanopolish_variants" ], "update_time": "2019-05-22", "versions": 2 @@ -73255,8 +88467,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "join1", - "datamash_ops" + "datamash_ops", + "join1" ], "update_time": "2019-05-13", "versions": 1 @@ -73281,8 +88493,8 @@ "tags": [], "tools": [ "bedtools_randombed", - "staramr_search", - "rbc_mafft" + "rbc_mafft", + "staramr_search" ], "update_time": "2019-05-03", "versions": 0 @@ -73326,10 +88538,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "mdanalysis_distance", - "mdanalysis_dihedral", - "mdanalysis_ramachandran_plot", "mdanalysis_rdf", + "mdanalysis_ramachandran_plot", + "mdanalysis_dihedral", + "mdanalysis_distance", "mdanalysis_cosine_analysis" ], "update_time": "2019-04-30", @@ -73351,19 +88563,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cardinal_preprocessing", - "cardinal_mz_images", - "tp_replace_in_column", - "cardinal_classification", - "cardinal_combine", - "maldi_quant_preprocessing", + "Filter1", + "join_files_on_column_fuzzy", "cardinal_segmentations", - "maldi_quant_peak_detection", + "cardinal_classification", "cardinal_filtering", - "join_files_on_column_fuzzy", + "maldi_quant_peak_detection", + "cardinal_mz_images", + "Grep1", + "maldi_quant_preprocessing", "cardinal_quality_report", - "Filter1", - "Grep1" + "tp_replace_in_column", + "cardinal_combine", + "cardinal_preprocessing" ], "update_time": "2019-04-26", "versions": 23 @@ -73373,8 +88585,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Expression profile clustering", "Expression analysis", + "Expression profile clustering", "Molecular dynamics" ], "edam_topic": [], @@ -73392,11 +88604,11 @@ "single-cell" ], "tools": [ - "raceid_filtnormconf", - "raceid_trajectory", + "raceid_inspectclusters", "raceid_clustering", + "raceid_filtnormconf", "raceid_inspecttrajectory", - "raceid_inspectclusters" + "raceid_trajectory" ], "update_time": "2019-04-17", "versions": 1 @@ -73420,8 +88632,8 @@ ], "tools": [ "tp_split_on_column", - "Cut1", "Remove beginning1", + "Cut1", "tp_replace_in_line" ], "update_time": "2019-04-11", @@ -73445,13 +88657,13 @@ "massspectrometryimaging" ], "tools": [ + "addName", "tp_split_on_column", - "Cut1", - "xpath", "tp_replace_in_line", - "addName", + "tp_cat", + "Cut1", "__RELABEL_FROM_FILE__", - "tp_cat" + "xpath" ], "update_time": "2019-04-11", "versions": 14 @@ -73461,12 +88673,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6e6cf59bfeb938bf", @@ -73479,20 +88691,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "gffcompare", - "fasta_merge_files_and_filter_unique_sequences", - "translate_bed", - "tp_replace_in_line", "freebayes", - "bed_to_protein_map", - "hisat2", - "query_tabular", "gffcompare_to_bed", + "query_tabular", "sqlite_to_tabular", - "stringtie", + "tp_replace_in_line", + "tp_cat", + "translate_bed", "tp_replace_in_column", - "custom_pro_db", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "gffcompare", + "stringtie", + "hisat2", + "bed_to_protein_map", + "custom_pro_db" ], "update_time": "2019-03-29", "versions": 2 @@ -73502,14 +88714,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence alignment", "Differential gene expression analysis", "Sequencing quality control", - "Sequence alignment", "Read summarisation", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "17ad465d9515cd25", @@ -73522,22 +88734,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_multijoin_tool", - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "volcanoplot", - "ggplot2_heatmap2", + "featurecounts", + "Cut1", + "multiqc", + "tp_cat", + "tp_multijoin_tool", "tp_sort_header_tool", + "volcanoplot", "scatterplot_rpy", - "Cut1", - "featurecounts", - "Filter1", + "tp_easyjoin_tool", "XY_Plot_1", - "hisat2", - "multiqc", - "deseq2", "stringtie", - "tp_cat" + "hisat2", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2019-03-16", "versions": 4 @@ -73547,11 +88759,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", "Visualisation", "Prediction and recognition", - "Formatting" + "Filtering", + "Formatting", + "Label-free quantification" ], "edam_topic": [], "id": "ba3a5d59b3879764", @@ -73565,16 +88777,16 @@ "tags": [], "tools": [ "msconvert", - "tp_replace_in_column", - "search_gui", - "peptide_shaker", - "Cut1", + "Filter1", + "query_tabular", "unipept", + "regex_replace", + "search_gui", "Remove beginning1", - "query_tabular", + "tp_replace_in_column", "flashlfq", - "Filter1", - "regex_replace" + "Cut1", + "peptide_shaker" ], "update_time": "2019-03-01", "versions": 4 @@ -73584,22 +88796,22 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence comparison", "Visualisation", - "Phylogenetic inference", + "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence comparison", + "Phylogenetic tree editing", + "Formatting", + "Sequence similarity search", "Read pre-processing", - "Taxonomic classification", - "Statistical calculation", - "Phylogenetic tree visualisation", + "Sequence composition calculation", + "Conversion", + "Sequence alignment analysis", + "Phylogenetic inference", "Sequence trimming", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "2cf09adb1ed6c3ec", @@ -73612,23 +88824,23 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bg_sortmerna", - "group_humann2_uniref_abundances_to_go", - "fastq_groomer", - "metaphlan2krona", "fastq_paired_end_joiner", - "metaphlan2", + "export2graphlan", "graphlan_annotate", + "bg_sortmerna", + "regex_replace", "combine_metaphlan2_humann2", - "graphlan", + "taxonomy_krona_chart", "trim_galore", - "format_metaphlan2_output", + "metaphlan2", "humann2_genefamilies_genus_level", - "taxonomy_krona_chart", - "humann2", + "group_humann2_uniref_abundances_to_go", + "graphlan", + "metaphlan2krona", "fastqc", - "regex_replace", - "export2graphlan" + "humann2", + "format_metaphlan2_output", + "fastq_groomer" ], "update_time": "2019-02-22", "versions": 3 @@ -73654,14 +88866,14 @@ ], "tools": [ "infernal_cmsearch", - "structure_to_gspan", - "viennarna_rnafold", "glob_report", "nspdk_sparse", "cmFinder", + "viennarna_rnafold", "locarna_best_subtree", - "preproc", "infernal_cmbuild", + "structure_to_gspan", + "preproc", "preMloc", "NSPDK_candidateClust" ], @@ -73689,14 +88901,14 @@ ], "tools": [ "infernal_cmsearch", - "structure_to_gspan", - "viennarna_rnafold", "glob_report", "nspdk_sparse", "cmFinder", + "viennarna_rnafold", "locarna_best_subtree", - "preproc", "infernal_cmbuild", + "structure_to_gspan", + "preproc", "preMloc", "NSPDK_candidateClust" ], @@ -73724,14 +88936,14 @@ ], "tools": [ "infernal_cmsearch", - "structure_to_gspan", - "viennarna_rnafold", "glob_report", "nspdk_sparse", "cmFinder", + "viennarna_rnafold", "locarna_best_subtree", - "preproc", "infernal_cmbuild", + "structure_to_gspan", + "preproc", "preMloc", "NSPDK_candidateClust" ], @@ -73743,16 +88955,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence composition calculation", + "RNA-Seq quantification", + "Read summarisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0de150b19102cb7e", @@ -73765,16 +88977,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "deeptools_bam_coverage", - "gffcompare", + "Filter1", + "featurecounts", "trimmomatic", "stringtie_merge", - "featurecounts", - "Filter1", - "hisat2", + "deeptools_bam_coverage", "fastqc", - "deseq2", - "stringtie" + "gffcompare", + "stringtie", + "hisat2", + "deseq2" ], "update_time": "2019-02-01", "versions": 3 @@ -73795,9 +89007,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "viennarna_rnaalifold", "viennarna_rnaplot", - "viennarna_rnafold" + "viennarna_rnafold", + "viennarna_rnaalifold" ], "update_time": "2019-02-01", "versions": 0 @@ -73843,9 +89055,9 @@ "visualization" ], "tools": [ + "tp_sort_header_tool", "cummeRbund", "Filter1", - "tp_sort_header_tool", "cummerbund_to_cuffdiff" ], "update_time": "2019-01-25", @@ -73873,12 +89085,12 @@ "model" ], "tools": [ - "RNAlien", + "rnaz", + "infernal_cmstat", "selectsequencesfrommsa", + "RNAlien", "cmv", - "rnaz", - "rbc_rnacode", - "infernal_cmstat" + "rbc_rnacode" ], "update_time": "2019-01-23", "versions": 0 @@ -73903,11 +89115,11 @@ "snorna" ], "tools": [ + "smf_utils_filter-by-energy", + "smf_utils_fix-fasta-headers", "smf_utils_extract-boxed-sequences", "smf_utils_find-boxes", - "smf_utils_fix-fasta-headers", - "smf_utils_estimate-energy", - "smf_utils_filter-by-energy" + "smf_utils_estimate-energy" ], "update_time": "2019-01-23", "versions": 0 @@ -73934,11 +89146,11 @@ ], "tools": [ "cat1", + "sort1", "AREsite2_REST", + "bedtools_intersectbed", "Cut1", - "sort1", - "addValue", - "bedtools_intersectbed" + "addValue" ], "update_time": "2019-01-23", "versions": 0 @@ -73948,8 +89160,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Multiple sequence alignment", - "Nucleic acid feature detection" + "Nucleic acid feature detection", + "Multiple sequence alignment" ], "edam_topic": [], "id": "5cd167ed9e159e73", @@ -73969,16 +89181,16 @@ "sequence" ], "tools": [ - "infernal_cmsearch", - "locarna_multiple", - "selectsequencesfrommsa", - "cmv", "rbc_mafft", - "rbc_rnacode", "rnaz", "infernal_cmstat", + "infernal_cmsearch", + "selectsequencesfrommsa", + "viennarna_rnaalifold", + "locarna_multiple", "infernal_cmbuild", - "viennarna_rnaalifold" + "cmv", + "rbc_rnacode" ], "update_time": "2019-01-23", "versions": 0 @@ -73988,9 +89200,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Primer removal", "Read pre-processing", + "Read mapping", "Sequence trimming" ], "edam_topic": [], @@ -74007,9 +89219,9 @@ "par-clip" ], "tools": [ - "trim_galore", "bowtie2", - "paralyzer" + "paralyzer", + "trim_galore" ], "update_time": "2019-01-23", "versions": 1 @@ -74019,9 +89231,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", "Pathway or network analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "12c80c5b5e2305d8", @@ -74039,12 +89251,12 @@ "pathway" ], "tools": [ + "heinz_scoring", "heinz_bum", + "heinz", "heinz_visualization", "Cut1", - "heinz", - "deseq2", - "heinz_scoring" + "deseq2" ], "update_time": "2019-01-17", "versions": 1 @@ -74054,20 +89266,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Gene functional annotation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", - "Gene functional annotation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9c7a218993788493", @@ -74085,22 +89297,22 @@ "name:star" ], "tools": [ - "ggplot2_heatmap2", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "rna_star", - "Cut1", - "join1", + "ggplot2_heatmap2", "featurecounts", - "rseqc_infer_experiment", - "gtftobed12", - "Filter1", + "goseq", + "Cut1", "multiqc", + "gtftobed12", + "tp_sort_header_tool", "ChangeCase", + "join1", "fastqc", - "deseq2", - "goseq", - "cutadapt" + "rna_star", + "cutadapt", + "rseqc_infer_experiment", + "deseq2" ], "update_time": "2019-01-17", "versions": 0 @@ -74151,10 +89363,10 @@ "classification" ], "tools": [ - "samtools_sort", - "blockclust", + "blockbuster", "tp_sort_header_tool", - "blockbuster" + "samtools_sort", + "blockclust" ], "update_time": "2019-01-17", "versions": 0 @@ -74165,10 +89377,10 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "RNA-Seq analysis", - "Differential gene expression analysis", "Gene expression analysis", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq quantification", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1ffc058273ab357e", @@ -74184,9 +89396,9 @@ "srna-seq" ], "tools": [ + "Filter1", "salmon", - "deseq2", - "Filter1" + "deseq2" ], "update_time": "2019-01-17", "versions": 0 @@ -74196,13 +89408,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment" + "Statistical calculation", + "Sequence alignment", + "Sequence trimming", + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "7734928ebc0a2654", @@ -74219,12 +89431,12 @@ "pre-processing" ], "tools": [ + "samtool_filter2", "trim_galore", "bedtools_bamtofastq", - "samtool_filter2", - "hisat2", + "fastq_manipulation", "fastqc", - "fastq_manipulation" + "hisat2" ], "update_time": "2019-01-17", "versions": 0 @@ -74235,13 +89447,13 @@ "doi": "", "edam_operation": [ "Statistical calculation", - "Sequence composition calculation", + "Sequence alignment", "Primer removal", - "Mapping", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Sequencing quality control", - "Sequence alignment" + "Mapping" ], "edam_topic": [], "id": "f5be5bcf9b9f171c", @@ -74258,26 +89470,26 @@ "clip-seq" ], "tools": [ - "deeptools_multi_bam_summary", - "bedtools_slopbed", - "umi_tools_dedup", - "__UNZIP_COLLECTION__", + "deeptools_plot_correlation", "wig_to_bigWig", - "umi_tools_extract", + "bctools_extract_crosslinked_nucleotides", + "bctools_extract_alignment_ends", + "rcas", "fastqc", + "rna_star", + "deeptools_multi_bam_summary", "Extract genomic DNA 1", - "deeptools_plot_correlation", - "meme_chip", - "rcas", + "cutadapt", + "__UNZIP_COLLECTION__", "bedtools_genomecoveragebed_bedgraph", - "peakachu", - "bctools_extract_alignment_ends", + "meme_chip", "deeptools_plot_fingerprint", - "rna_star", - "tp_awk_tool", + "umi_tools_extract", "bedtools_sortbed", - "cutadapt", - "bctools_extract_crosslinked_nucleotides" + "peakachu", + "bedtools_slopbed", + "umi_tools_dedup", + "tp_awk_tool" ], "update_time": "2019-01-17", "versions": 0 @@ -74287,16 +89499,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence composition calculation", + "RNA-Seq quantification", + "Read summarisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "f026c4b8341ff94c", @@ -74313,16 +89525,16 @@ "assembly" ], "tools": [ - "deeptools_bam_coverage", - "gffcompare", + "Filter1", + "featurecounts", "trimmomatic", "stringtie_merge", - "featurecounts", - "Filter1", - "hisat2", + "deeptools_bam_coverage", "fastqc", - "deseq2", - "stringtie" + "gffcompare", + "stringtie", + "hisat2", + "deseq2" ], "update_time": "2019-01-17", "versions": 0 @@ -74347,10 +89559,10 @@ "tools": [ "gmx_solvate", "gmx_npt", + "gmx_setup", "gmx_nvt", "gmx_md", - "gmx_em", - "gmx_setup" + "gmx_em" ], "update_time": "2019-01-09", "versions": 9 @@ -74360,11 +89572,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", + "Validation", "Sequencing quality control", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "44c5999436da5f1e", @@ -74379,11 +89591,11 @@ "clip-explorer" ], "tools": [ - "je_demultiplex", - "umi_tools_extract", - "__UNZIP_COLLECTION__", "multiqc", - "cutadapt" + "umi_tools_extract", + "je_demultiplex", + "cutadapt", + "__UNZIP_COLLECTION__" ], "update_time": "2018-12-17", "versions": 9 @@ -74393,11 +89605,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", + "Validation", "Sequencing quality control", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "a1e09c648d8f1fc7", @@ -74412,11 +89624,11 @@ "clip-explorer" ], "tools": [ - "je_demultiplex", - "umi_tools_extract", - "__UNZIP_COLLECTION__", "multiqc", - "cutadapt" + "umi_tools_extract", + "je_demultiplex", + "cutadapt", + "__UNZIP_COLLECTION__" ], "update_time": "2018-12-17", "versions": 8 @@ -74466,11 +89678,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Extract genomic DNA 1", + "blockclust", "infernal_cmsearch", - "tp_sort_header_tool", "samtools_sort", - "blockclust", + "tp_sort_header_tool", + "Extract genomic DNA 1", "blockbuster" ], "update_time": "2018-12-10", @@ -74481,12 +89693,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "c64b219b4031fabd", @@ -74499,11 +89711,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", "featurecounts", - "umi_tools_count", + "bamFilter", "umi_tools_extract", - "bamFilter" + "rna_star", + "umi_tools_count" ], "update_time": "2018-12-05", "versions": 2 @@ -74524,10 +89736,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_sort", - "blockclust", + "blockbuster", "tp_sort_header_tool", - "blockbuster" + "samtools_sort", + "blockclust" ], "update_time": "2018-11-27", "versions": 11 @@ -74551,11 +89763,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2018-11-19", "versions": 1 @@ -74579,11 +89791,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2018-11-19", "versions": 3 @@ -74604,10 +89816,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "pep_pointer", "peptidegenomiccoordinate", "tab2fasta", "ncbi_blastp_wrapper", + "pep_pointer", "query_tabular" ], "update_time": "2018-11-13", @@ -74618,8 +89830,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "b89cf3cb6a25c999", @@ -74632,14 +89844,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "query_tabular", "fasta2tab", "search_gui", - "peptide_shaker", - "Cut1", "Convert characters1", "Grouping1", "mz_to_sqlite", - "query_tabular" + "Cut1", + "peptide_shaker" ], "update_time": "2018-11-13", "versions": 0 @@ -74663,11 +89875,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2018-11-13", "versions": 0 @@ -74691,11 +89903,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2018-11-13", "versions": 1 @@ -74705,19 +89917,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", "DNA mapping", + "Statistical calculation", + "Genome assembly", "Chimera detection", - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", - "Genome assembly", "Sequence comparison", - "Gene prediction", - "Primer removal", + "Sequence similarity search", "Read pre-processing", - "Sequence trimming", - "Statistical calculation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Sequence trimming" ], "edam_topic": [], "id": "401746888e8b3aa8", @@ -74730,10 +89942,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bg_sortmerna", - "trim_galore", "fraggenescan", + "bg_sortmerna", "megahit", + "trim_galore", "fastqc", "vsearch_dereplication" ], @@ -74745,19 +89957,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", "DNA mapping", + "Statistical calculation", + "Genome assembly", "Chimera detection", - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", - "Genome assembly", "Sequence comparison", - "Gene prediction", - "Primer removal", + "Sequence similarity search", "Read pre-processing", - "Sequence trimming", - "Statistical calculation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Sequence trimming" ], "edam_topic": [], "id": "9382f9bbbdddb5ad", @@ -74770,16 +89982,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "fastq_to_tabular", + "fraggenescan", "tabular_to_fastq", "bg_sortmerna", "fasta2tab", - "tp_cut_tool", - "join1", "trim_galore", - "fastq_to_tabular", - "fraggenescan", "metaspades", + "join1", "fastqc", + "tp_cut_tool", "vsearch_dereplication" ], "update_time": "2018-11-01", @@ -74801,11 +90013,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "fastq_to_tabular", "tabular_to_fastq", "fasta2tab", - "tp_cut_tool", "join1", - "fastq_to_tabular" + "tp_cut_tool" ], "update_time": "2018-10-18", "versions": 1 @@ -74815,19 +90027,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", "DNA mapping", + "Statistical calculation", + "Genome assembly", "Chimera detection", - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", - "Genome assembly", "Sequence comparison", - "Gene prediction", - "Primer removal", + "Sequence similarity search", "Read pre-processing", - "Sequence trimming", - "Statistical calculation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Sequence trimming" ], "edam_topic": [], "id": "a8417c63e9e22afb", @@ -74840,13 +90052,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bg_sortmerna", - "metaphlan2", - "trim_galore", "fastq_combiner", "fraggenescan", - "metaspades", + "bg_sortmerna", "megahit", + "trim_galore", + "metaphlan2", + "metaspades", "fastqc", "vsearch_dereplication" ], @@ -74872,13 +90084,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "fastq_to_tabular", + "fraggenescan", "tabular_to_fastq", "fasta2tab", - "tp_cut_tool", + "metaspades", "join1", - "fastq_to_tabular", - "fraggenescan", - "metaspades" + "tp_cut_tool" ], "update_time": "2018-10-16", "versions": 1 @@ -74902,9 +90114,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "metaspades", "fastq_combiner", "fraggenescan", - "metaspades", "megahit" ], "update_time": "2018-10-16", @@ -74963,23 +90175,23 @@ "doi": "", "edam_operation": [ "DNA mapping", + "Visualisation", + "Statistical calculation", "Chimera detection", - "Sequence alignment analysis", - "Conversion", - "Sequence similarity search", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", - "Formatting", "Sequence comparison", - "Visualisation", - "Phylogenetic inference", - "Primer removal", + "Phylogenetic tree editing", + "Formatting", + "Sequence similarity search", "Read pre-processing", - "Taxonomic classification", - "Statistical calculation", - "Phylogenetic tree visualisation", + "Sequence composition calculation", + "Conversion", + "Sequence alignment analysis", + "Phylogenetic inference", "Sequence trimming", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "9cbba5de2cbeeb0f", @@ -74992,21 +90204,21 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bg_sortmerna", - "group_humann2_uniref_abundances_to_go", - "metaphlan2krona", - "metaphlan2", + "export2graphlan", "graphlan_annotate", + "bg_sortmerna", "combine_metaphlan2_humann2", - "graphlan", + "taxonomy_krona_chart", "trim_galore", - "format_metaphlan2_output", + "metaphlan2", "humann2_genefamilies_genus_level", - "taxonomy_krona_chart", - "humann2", + "group_humann2_uniref_abundances_to_go", + "graphlan", + "metaphlan2krona", "fastqc", - "vsearch_dereplication", - "export2graphlan" + "humann2", + "format_metaphlan2_output", + "vsearch_dereplication" ], "update_time": "2018-09-26", "versions": 0 @@ -75016,15 +90228,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", "Sequence clustering", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Phylogenetic tree generation (from molecular sequences)", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "ce21961260fe4351", @@ -75041,35 +90253,35 @@ "16s" ], "tools": [ - "mothur_cluster_split", + "mothur_get_oturep", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "fasttree", + "collapse_dataset", + "mothur_count_groups", + "mothur_classify_seqs", + "mothur_pcoa", "mothur_dist_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_heatmap_bin", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_pcoa", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_heatmap_bin", + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_summary_single", + "mothur_cluster_split", + "mothur_count_seqs", "mothur_make_shared", "mothur_pre_cluster", - "mothur_get_oturep", - "mothur_summary_single", - "mothur_taxonomy_to_krona", - "mothur_venn", - "fasttree", - "mothur_sub_sample", - "mothur_classify_seqs", - "collapse_dataset", - "mothur_filter_seqs", "mothur_chimera_vsearch", - "mothur_summary_seqs", - "mothur_rarefaction_single", - "mothur_align_seqs", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_remove_seqs", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", "XY_Plot_1" ], @@ -75092,18 +90304,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "ctb_online_data_fetch", "cat1", + "Filter1", "sed_stream_editor", - "Grep1", + "ctb_change_title", + "ctb_online_data_fetch", "Cut1", + "Grep1", + "openbabel_compound_convert", + "ctb_remIons", "mergeCols1", "addValue", - "bg_uniq", - "openbabel_compound_convert", - "Filter1", - "ctb_change_title", - "ctb_remIons" + "bg_uniq" ], "update_time": "2018-09-03", "versions": 4 @@ -75135,19 +90347,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Visualisation", + "Statistical calculation", "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", + "Sequence assembly", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Validation" + "Sequence assembly validation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "579ff83177c5ee09", @@ -75162,13 +90374,13 @@ "asaim" ], "tools": [ - "valet", + "bowtie2", + "multiqc", "trim_galore", "quast", "metaspades", - "multiqc", "fastqc", - "bowtie2" + "valet" ], "update_time": "2018-08-03", "versions": 3 @@ -75178,19 +90390,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Visualisation", + "Statistical calculation", "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", + "Sequence assembly", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Validation" + "Sequence assembly validation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "1524b189069b42a5", @@ -75205,13 +90417,13 @@ "asaim" ], "tools": [ - "valet", - "trim_galore", - "quast", + "bowtie2", "multiqc", "megahit", + "trim_galore", + "quast", "fastqc", - "bowtie2" + "valet" ], "update_time": "2018-08-03", "versions": 4 @@ -75222,23 +90434,23 @@ "doi": "", "edam_operation": [ "DNA mapping", + "Visualisation", + "Statistical calculation", "Chimera detection", - "Sequence alignment analysis", - "Conversion", - "Sequence similarity search", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", - "Formatting", "Sequence comparison", - "Visualisation", - "Phylogenetic inference", - "Primer removal", + "Phylogenetic tree editing", + "Formatting", + "Sequence similarity search", "Read pre-processing", - "Taxonomic classification", - "Statistical calculation", - "Phylogenetic tree visualisation", + "Sequence composition calculation", + "Conversion", + "Sequence alignment analysis", + "Phylogenetic inference", "Sequence trimming", - "Phylogenetic tree editing" + "Phylogenetic tree visualisation", + "Taxonomic classification" ], "edam_topic": [], "id": "c3aa516e78ca4191", @@ -75251,20 +90463,20 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bg_sortmerna", - "metaphlan2krona", - "metaphlan2", + "export2graphlan", "graphlan_annotate", + "bg_sortmerna", "combine_metaphlan2_humann2", - "graphlan", + "taxonomy_krona_chart", "trim_galore", - "format_metaphlan2_output", + "metaphlan2", "humann2_genefamilies_genus_level", - "taxonomy_krona_chart", - "humann2", + "graphlan", + "metaphlan2krona", "fastqc", - "vsearch_dereplication", - "export2graphlan" + "humann2", + "format_metaphlan2_output", + "vsearch_dereplication" ], "update_time": "2018-08-03", "versions": 4 @@ -75274,13 +90486,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "83a0c1ba280785e6", @@ -75294,20 +90506,20 @@ "tags": [], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", - "mothur_chimera_uchime", + "mothur_classify_otu", "mothur_screen_seqs", - "mothur_classify_seqs", + "mothur_pre_cluster", "mothur_remove_lineage", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_chimera_uchime", + "mothur_filter_seqs", "mothur_remove_seqs", + "mothur_make_contigs", + "mothur_cluster_split", "mothur_count_seqs", "mothur_unique_seqs", - "mothur_filter_seqs", - "mothur_classify_otu", - "mothur_summary_seqs", - "mothur_make_contigs", - "mothur_align_seqs" + "mothur_classify_seqs" ], "update_time": "2018-08-02", "versions": 0 @@ -75317,13 +90529,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "c55388a8fbfd7381", @@ -75337,10 +90549,10 @@ "tags": [], "tools": [ "mothur_screen_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", "ncbi_blastn_wrapper", - "mothur_make_contigs" + "mothur_make_contigs", + "mothur_count_seqs", + "mothur_unique_seqs" ], "update_time": "2018-08-02", "versions": 0 @@ -75363,10 +90575,10 @@ "tools": [ "cat1", "fasta2tab", + "comp1", "filter_by_fasta_ids", - "Cut1", "tp_sorted_uniq", - "comp1" + "Cut1" ], "update_time": "2018-06-26", "versions": 0 @@ -75377,10 +90589,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "d22dac11eba8c5a3", @@ -75394,11 +90606,11 @@ "tags": [], "tools": [ "EMBOSS: transeq101", - "Cut1", "get_feature_info", "ncbi_blastp_wrapper", "get_sequences", - "uniprot" + "uniprot", + "Cut1" ], "update_time": "2018-06-26", "versions": 1 @@ -75408,14 +90620,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Phylogenetic analysis", - "Local alignment", "Sequence alignment", "Phylogenetic inference (from molecular sequences)", + "Local alignment", + "Phylogenetic analysis", + "Sequence alignment analysis", + "Sequence analysis", "Global alignment", - "Phylogenetic tree visualisation", - "Sequence analysis" + "Phylogenetic tree visualisation" ], "edam_topic": [], "id": "2cec6a39cd496f09", @@ -75428,18 +90640,18 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "filter_by_fasta_ids", - "blast_parser", + "ncbi_makeblastdb", "EMBOSS: transeq101", + "blast_parser", "ncbi_blastp_wrapper", - "trimmer", - "t_coffee", + "EMBOSS: tranalign100", + "hcluster_sg", "hcluster_sg_parser", + "filter_by_fasta_ids", "treebest_best", - "hcluster_sg", - "ncbi_makeblastdb", - "EMBOSS: tranalign100", - "gafa" + "gafa", + "t_coffee", + "trimmer" ], "update_time": "2018-06-26", "versions": 0 @@ -75527,8 +90739,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "samtools_filter", "bedtools_bamtofastq", + "samtools_filter", "hisat2" ], "update_time": "2018-04-29", @@ -75539,9 +90751,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -75555,12 +90767,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "bwa_mem", - "hicexplorer_hicfindtads", - "hicexplorer_hicplottads", - "hicexplorer_hicsummatrices", "hicexplorer_hiccorrectmatrix", + "hicexplorer_hicplottads", + "hicexplorer_hicfindtads", "hicexplorer_hicbuildmatrix", + "hicexplorer_hicsummatrices", + "bwa_mem", "hicexplorer_hicpca" ], "update_time": "2018-04-29", @@ -75571,13 +90783,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Validation", "Sequencing quality control", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "59b274da8df01ead", @@ -75591,8 +90803,8 @@ "tags": [], "tools": [ "fastqc", - "trim_galore", - "multiqc" + "multiqc", + "trim_galore" ], "update_time": "2018-03-23", "versions": 14 @@ -75602,11 +90814,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Sequencing quality control", - "Sequence alignment", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "c6b22fc33b569c8f", @@ -75619,13 +90831,13 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rna_star", - "umi_tools_dedup", + "samtools_stats", "featurecounts", + "multiqc", + "umi_tools_dedup", "tp_sed_tool", - "samtools_stats", "collection_column_join", - "multiqc" + "rna_star" ], "update_time": "2018-03-21", "versions": 19 @@ -75648,9 +90860,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "umi_tools_extract", "je_demultiplex", - "tp_cat" + "tp_cat", + "umi_tools_extract" ], "update_time": "2018-03-17", "versions": 11 @@ -75674,14 +90886,14 @@ "mimodd" ], "tools": [ - "mimodd_varreport", + "snpEff", "snpEff_download", - "mimodd_varextract", "tp_find_and_replace", + "mimodd_varreport", + "mimodd_varextract", + "mimodd_varcall", "mimodd_vcf_filter", - "snpEff", - "mimodd_map", - "mimodd_varcall" + "mimodd_map" ], "update_time": "2018-03-09", "versions": 20 @@ -75691,10 +90903,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -75713,8 +90925,8 @@ "qiime_pick_open_reference_otus", "qiime_split_libraries_fastq", "qiime_core_diversity", - "qiime_count_seqs", - "qiime_validate_mapping_file" + "qiime_validate_mapping_file", + "qiime_count_seqs" ], "update_time": "2018-01-17", "versions": 0 @@ -75724,25 +90936,25 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Sequence generation", - "Probabilistic sequence generation", - "Sequencing quality control", - "Phylogenetic analysis", - "Formatting", "Visualisation", - "Data retrieval", + "Sequence motif recognition", "Database search", - "Protein feature detection", - "Sequence profile generation", "Format validation", + "Sequencing quality control", + "Formatting", + "Multiple sequence alignment", + "Conversion", "Sequence database search", - "Demultiplexing", + "Sequence profile generation", + "Probabilistic sequence generation", + "Protein feature detection", "Gene prediction", - "Sequence motif recognition", "Statistical calculation", - "Taxonomic classification", - "Multiple sequence alignment" + "Phylogenetic analysis", + "Demultiplexing", + "Sequence generation", + "Data retrieval", + "Taxonomic classification" ], "edam_topic": [], "id": "58955868b504c60d", @@ -75758,15 +90970,15 @@ ], "tools": [ "seq_filter_by_id", - "qiime_pick_closed_reference_otus", - "interproscan", - "trimmomatic", - "tp_awk_tool", - "hmmer_hmmsearch", "fraggenescan", + "hmmer_hmmsearch", + "trimmomatic", "hmmer_hmmbuild", + "tp_cat", + "interproscan", + "qiime_pick_closed_reference_otus", "cshl_fastq_to_fasta", - "tp_cat" + "tp_awk_tool" ], "update_time": "2018-01-17", "versions": 0 @@ -75776,9 +90988,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Enrichment analysis", "Peak calling", - "Gene regulatory network analysis" + "Gene regulatory network analysis", + "Enrichment analysis" ], "edam_topic": [], "id": "604b67c8525637bc", @@ -75806,10 +91018,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Formatting", + "Statistical calculation", "Variant calling", - "Statistical calculation" + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "2f1ee01aeee2b9f0", @@ -75824,17 +91036,17 @@ "exome" ], "tools": [ - "sam_merge2", - "picard_MarkDuplicates", + "bowtie2", "picard_ReorderSam", + "freebayes", + "snpEff", "gemini_load", "gemini_query", - "snpEff", - "freebayes", + "sam_merge2", "vcfallelicprimitives", - "bowtie2", "snpSift_annotate", - "snpSift_filter" + "snpSift_filter", + "picard_MarkDuplicates" ], "update_time": "2017-09-22", "versions": 11 @@ -75881,18 +91093,18 @@ "published" ], "tools": [ + "Filter1", "wolf_psort", + "get_subontology_from", + "uniprot", + "term_id_vs_term_name", + "Grep1", + "Convert characters1", + "comp1", "tp_easyjoin_tool", "tp_cut_tool", "tp_sorted_uniq", - "comp1", - "uniprot", - "Convert characters1", - "bg_uniq", - "term_id_vs_term_name", - "get_subontology_from", - "Filter1", - "Grep1" + "bg_uniq" ], "update_time": "2016-03-18", "versions": 6 @@ -75913,12 +91125,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "comp1", - "bg_uniq", - "term_id_vs_term_name", "get_subontology_from", - "Grep1" + "term_id_vs_term_name", + "Grep1", + "comp1", + "tp_easyjoin_tool", + "bg_uniq" ], "update_time": "2016-03-11", "versions": 28 @@ -75939,9 +91151,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", + "mergeCols1", "addValue", - "mergeCols1" + "Cut1" ], "update_time": "2016-02-24", "versions": 1 @@ -75962,12 +91174,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "comp1", - "bg_uniq", - "term_id_vs_term_name", "get_subontology_from", - "Grep1" + "term_id_vs_term_name", + "Grep1", + "comp1", + "tp_easyjoin_tool", + "bg_uniq" ], "update_time": "2016-02-22", "versions": -1 @@ -75988,12 +91200,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_easyjoin_tool", - "comp1", - "bg_uniq", - "term_id_vs_term_name", "get_subontology_from", - "Grep1" + "term_id_vs_term_name", + "Grep1", + "comp1", + "tp_easyjoin_tool", + "bg_uniq" ], "update_time": "2016-01-27", "versions": 0 @@ -76003,9 +91215,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", "Formatting", - "Variant calling", - "Statistical calculation" + "Variant calling" ], "edam_topic": [], "id": "ad609d1a3de251f5", @@ -76018,16 +91230,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "sam_merge2", - "picard_MarkDuplicates", "picard_ReorderSam", + "freebayes", + "snpEff", "gemini_load", "gemini_query", - "snpEff", - "freebayes", + "sam_merge2", "vcfallelicprimitives", "snpSift_annotate", - "snpSift_filter" + "snpSift_filter", + "picard_MarkDuplicates" ], "update_time": "2015-10-12", "versions": 0 @@ -76051,15 +91263,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "Paste1", + "bowtie2", "rseqc_inner_distance", - "tp_awk_tool", - "tp_find_and_replace", - "rseqc_infer_experiment", "Show beginning1", - "bowtie2", + "tp_find_and_replace", + "tp_cat", "Grep1", - "Paste1", - "tp_cat" + "rseqc_infer_experiment", + "tp_awk_tool" ], "update_time": "2015-10-07", "versions": 12 @@ -76070,10 +91282,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "1031e4c4f18e020e", @@ -76086,11 +91298,11 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "tab2fasta", + "EMBOSS: shuffleseq87", "fasta2tab", "Cut1", - "tab2fasta", - "addValue", - "EMBOSS: shuffleseq87" + "addValue" ], "update_time": "2015-07-26", "versions": 3 @@ -76111,12 +91323,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Count1", - "get_flanks1", "cshl_awk_tool", - "barchart_gnuplot", + "gops_intersect_1", + "Count1", "tp_replace_in_column", - "gops_intersect_1" + "get_flanks1", + "barchart_gnuplot" ], "update_time": "2015-07-17", "versions": 0 @@ -76137,12 +91349,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Count1", - "get_flanks1", "cshl_awk_tool", - "charts", + "gops_intersect_1", + "Count1", "tp_replace_in_column", - "gops_intersect_1" + "charts", + "get_flanks1" ], "update_time": "2015-07-17", "versions": 1 @@ -76163,9 +91375,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "blockbuster", "sort1", - "blockclust", - "blockbuster" + "blockclust" ], "update_time": "2015-06-26", "versions": 0 @@ -76188,10 +91400,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Extract genomic DNA 1", - "infernal_cmsearch", "sort1", "blockclust", + "infernal_cmsearch", + "Extract genomic DNA 1", "blockbuster" ], "update_time": "2015-06-26", @@ -76202,21 +91414,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Protein feature detection", - "Operation", - "Sequence alignment analysis", - "Global alignment", - "Sequence annotation", - "Differential gene expression analysis", - "Local alignment", - "Sequence alignment", - "Ab-initio gene prediction", "Gene prediction", - "Sequence motif recognition", - "Homology-based gene prediction", "Sequence clustering", + "Homology-based gene prediction", + "Sequence motif recognition", + "Sequence alignment", + "Differential gene expression analysis", + "Gene functional annotation", + "Local alignment", + "Sequence alignment analysis", "Sequence analysis", - "Gene functional annotation" + "Global alignment", + "Protein feature detection", + "Operation", + "Ab-initio gene prediction", + "Sequence annotation" ], "edam_topic": [], "id": "33312e5643279e8a", @@ -76229,22 +91441,22 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "interproscan", - "blastxml_to_top_descr", - "seq_filter_by_id", - "wolf_psort", - "blast2go", - "Grep1", "tmhmm2", - "ncbi_blastp_wrapper", - "aragorn_trna", - "antismash", - "megablast_xml_parser", - "seq_composition", "Filter1", + "wolf_psort", "EMBOSS: geecee41", + "antismash", + "ncbi_blastp_wrapper", + "seq_composition", "fasta_compute_length", - "augustus" + "blast2go", + "Grep1", + "blastxml_to_top_descr", + "megablast_xml_parser", + "interproscan", + "augustus", + "seq_filter_by_id", + "aragorn_trna" ], "update_time": "2015-06-23", "versions": 1 @@ -76255,10 +91467,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "0ed8817a90caa2b1", @@ -76271,14 +91483,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rmcontamination", - "fasta2tab", "EMBOSS: transeq101", - "Grep1", - "tp_cut_tool", "tab2fasta", "build_ucsc_custom_track_1", - "tp_replace_in_column" + "fasta2tab", + "Grep1", + "rmcontamination", + "tp_replace_in_column", + "tp_cut_tool" ], "update_time": "2015-06-23", "versions": -1 @@ -76289,10 +91501,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "9275d0c90a8713d6", @@ -76305,12 +91517,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rmcontamination", - "aragorn_trna", - "glimmer_knowlegde-based", - "seq_composition", "EMBOSS: geecee41", - "trnascan" + "seq_composition", + "trnascan", + "glimmer_knowlegde-based", + "rmcontamination", + "aragorn_trna" ], "update_time": "2015-06-23", "versions": -1 @@ -76333,10 +91545,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "bedtools_sortbed", "cat1", "Cut1", - "Add_a_column1", - "bedtools_sortbed" + "Add_a_column1" ], "update_time": "2015-06-12", "versions": 1 @@ -76357,15 +91569,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "gops_coverage_1", + "Paste1", "cat1", + "Filter1", "Add_a_column1", "Summary_Statistics1", "Cut1", - "gops_coverage_1", "addValue", - "barchart_gnuplot", - "Filter1", - "Paste1" + "barchart_gnuplot" ], "update_time": "2015-06-01", "versions": 3 @@ -76376,12 +91588,12 @@ "doi": "", "edam_operation": [ "Peak calling", + "Sequence composition calculation", "Gene regulatory network analysis", "Statistical calculation", - "Sequence composition calculation", + "Sequencing quality control", "Read mapping", "Enrichment analysis", - "Sequencing quality control", "Formatting" ], "edam_topic": [], @@ -76396,18 +91608,18 @@ "tags": [], "tools": [ "deeptools_computeGCBias", - "samtools_flagstat", - "picard_MarkDuplicates", + "bowtie2", + "macs2_callpeak", "deeptools_bamFingerprint", - "PicardInsertSize", "deeptools_bamCoverage", + "PicardInsertSize", "deeptools_bamCompare", - "deeptools_heatmapper", "deeptools_computeMatrix", - "deeptools_bamCorrelate", "fastqc", - "macs2_callpeak", - "bowtie2" + "samtools_flagstat", + "deeptools_bamCorrelate", + "deeptools_heatmapper", + "picard_MarkDuplicates" ], "update_time": "2015-05-31", "versions": 22 @@ -76428,10 +91640,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "tp_awk_tool", - "sort1", "sed_stream_editor", - "tp_easyjoin_tool" + "sort1", + "tp_easyjoin_tool", + "tp_awk_tool" ], "update_time": "2015-05-18", "versions": 6 @@ -76442,10 +91654,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "eaf3c4d97399e673", @@ -76458,9 +91670,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "glimmer_build-icm", "EMBOSS: transeq101", - "glimmer_knowlegde-based", - "glimmer_build-icm" + "glimmer_knowlegde-based" ], "update_time": "2015-05-12", "versions": 0 @@ -76481,10 +91693,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "seq_filter_by_id", "tmhmm2", "Filter1", - "signalp3" + "signalp3", + "seq_filter_by_id" ], "update_time": "2015-05-12", "versions": 0 @@ -76505,12 +91717,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "sort1", "Add_a_column1", - "Cut1", "ncbi_tblastn_wrapper", - "sort1", + "gops_intersect_1", "Grouping1", - "gops_intersect_1" + "Cut1" ], "update_time": "2015-03-17", "versions": 3 @@ -76554,8 +91766,8 @@ "tools": [ "samtools_mpileup", "snpEff", - "snpSift_annotate", "bcftools_view", + "snpSift_annotate", "snpSift_filter" ], "update_time": "2014-11-20", @@ -76580,9 +91792,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "picard_ReorderSam", + "rgPicardMarkDups", "bowtie2", - "rgPicardMarkDups" + "picard_ReorderSam" ], "update_time": "2014-11-13", "versions": 0 @@ -76603,8 +91815,8 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Count1", "gops_intersect_1", + "Count1", "barchart_gnuplot" ], "update_time": "2014-11-03", @@ -76626,14 +91838,14 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "gemini_pathways", "gemini_de_novo", "gemini_roh", - "gemini_recessive_and_dominant", - "gemini_interactions", - "gemini_pathways", "gemini_lof_sieve", - "gemini_comp_hets", - "gemini_stats" + "gemini_interactions", + "gemini_stats", + "gemini_recessive_and_dominant", + "gemini_comp_hets" ], "update_time": "2014-09-30", "versions": 1 @@ -76643,8 +91855,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "ffe93ec81afefd09", @@ -76657,12 +91869,12 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "vt_normalize", "freebayes", "snpEff", "vcfallelicprimitives", "snpSift_annotate", - "snpSift_filter" + "snpSift_filter", + "vt_normalize" ], "update_time": "2014-09-25", "versions": 5 @@ -76672,11 +91884,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Formatting", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "c377b21d2be45a57", @@ -76689,10 +91901,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "rgPicardMarkDups", "picard_ReorderSam", - "bwa_mem", "sam_to_bam", - "rgPicardMarkDups" + "bwa_mem" ], "update_time": "2014-09-25", "versions": -1 @@ -76702,8 +91914,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "4a89ddab941c6819", @@ -76787,9 +91999,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", "sort1", - "cshl_uniq_tool" + "cshl_uniq_tool", + "Cut1" ], "update_time": "2014-09-22", "versions": 0 @@ -76835,19 +92047,19 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "picard_ReorderSam", + "bowtie2", "gatk2_realigner_target_creator", - "rgPicardMarkDups", - "gatk2_indel_realigner", - "gatk2_reduce_reads", - "cshl_cut_tool", + "picard_ReorderSam", + "gatk2_haplotype_caller", "gatk2_variant_recalibrator", - "gatk2_variant_apply_recalibration", - "vcftools_merge", - "bowtie2", + "gatk2_reduce_reads", + "gatk2_indel_realigner", "gatk2_base_recalibrator", - "gatk2_haplotype_caller", - "gatk2_print_reads" + "rgPicardMarkDups", + "gatk2_variant_apply_recalibration", + "cshl_cut_tool", + "gatk2_print_reads", + "vcftools_merge" ], "update_time": "2014-08-11", "versions": 31 @@ -76857,9 +92069,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Differential gene expression analysis", "Gene prediction", - "Sequence clustering" + "Sequence clustering", + "Differential gene expression analysis" ], "edam_topic": [], "id": "0461bbd1f96292e2", @@ -76872,9 +92084,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rmcontamination", - "antismash", "scaffold2fasta", + "antismash", + "rmcontamination", "prokaryotic_ncbi_submission" ], "update_time": "2014-03-24", @@ -76885,10 +92097,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Variant calling" + "Statistical calculation", + "Variant calling", + "Sequencing quality control" ], "edam_topic": [], "id": "4412f7223a557b48", @@ -76901,16 +92113,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "naive_variant_caller", - "sam_merge2", "allele_counts_1", + "naive_variant_caller", + "Filter1", "freebayes", + "sam_bw_filter", + "sam_merge2", "bwa_wrapper", + "sam_to_bam", "fastqc", - "Filter1", - "sam_to_bam" + "picard_ARRG" ], "update_time": "2013-11-17", "versions": 0 @@ -76920,9 +92132,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Differential gene expression analysis", "Gene prediction", - "Sequence clustering" + "Sequence clustering", + "Differential gene expression analysis" ], "edam_topic": [], "id": "edbaf66c1e97ebdb", @@ -76935,10 +92147,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "rmcontamination", - "antismash", "scaffold2fasta", - "eukaryotic_ncbi_submission" + "eukaryotic_ncbi_submission", + "antismash", + "rmcontamination" ], "update_time": "2013-10-25", "versions": 3 @@ -76959,10 +92171,10 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", - "Filter1", "wig_to_bigWig", - "Add_a_column1" + "Filter1", + "Add_a_column1", + "Cut1" ], "update_time": "2013-09-26", "versions": 2 @@ -76988,8 +92200,8 @@ "bam" ], "tools": [ - "bamFingerprint", "bamCorrelate_deepTools", + "bamFingerprint", "computeGCBias" ], "update_time": "2013-08-09", @@ -77038,9 +92250,9 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "dt_profiler", + "computeMatrix", "bamCoverage_deepTools", - "computeMatrix" + "dt_profiler" ], "update_time": "2013-08-09", "versions": 6 @@ -77068,10 +92280,10 @@ "log2ratio" ], "tools": [ - "heatmapper_deepTools", + "bamCompare_deepTools", "Grep1", "computeMatrix", - "bamCompare_deepTools" + "heatmapper_deepTools" ], "update_time": "2013-08-09", "versions": 2 @@ -77092,15 +92304,15 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "cat1", "bedtools_intersectbed_bam", + "cat1", + "cshl_uniq_tool", + "sort1", "wc_gnu", + "cshl_awk_tool", "Count1", - "sort1", "addValue", - "cshl_awk_tool", - "barchart_gnuplot", - "cshl_uniq_tool" + "barchart_gnuplot" ], "update_time": "2013-02-22", "versions": 1 @@ -77121,16 +92333,16 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ + "gops_coverage_1", + "Paste1", "cat1", + "Filter1", "Add_a_column1", + "cshl_grep_tool", "Summary_Statistics1", "Cut1", - "gops_coverage_1", "addValue", - "barchart_gnuplot", - "cshl_grep_tool", - "Filter1", - "Paste1" + "barchart_gnuplot" ], "update_time": "2013-02-21", "versions": 2 @@ -77151,26 +92363,86 @@ "source": "https://usegalaxy.eu", "tags": [], "tools": [ - "Cut1", - "addValue", - "Remove beginning1", + "Paste1", "Grep1", - "Paste1" + "Remove beginning1", + "Cut1", + "addValue" ], "update_time": "2013-02-07", "versions": 1 }, + { + "create_time": "2024-12-19", + "creators": [ + "Galaxy", + "VGP" + ], + "doi": "", + "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Phasing", + "Transcriptome assembly", + "k-mer counting", + "Read pre-processing", + "De-novo assembly", + "Sequence trimming", + "Sequence assembly validation", + "Validation", + "Data handling" + ], + "edam_topic": [], + "id": "498a8c6329ca5728", + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://usegalaxy.org/published/workflow?id=498a8c6329ca5728", + "name": "Assembly-Hifi-Trio-phasing-VGP5 (release v0.4)", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.org", + "tags": [ + "vgp", + "reviewed" + ], + "tools": [ + "__EXTRACT_DATASET__", + "tp_find_and_replace", + "join1", + "tp_grep_tool", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", + "Convert characters1", + "busco", + "cutadapt", + "hifiasm", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", + "Cut1", + "tp_awk_tool" + ], + "update_time": "2024-12-19", + "versions": 1 + }, { "create_time": "2024-09-16", "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Scatter plot plotting", - "Statistical calculation", + "Pairwise sequence alignment", "Sequence composition calculation", + "Statistical calculation", + "Scatter plot plotting", + "Data handling", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting" ], "edam_topic": [], @@ -77191,14 +92463,14 @@ "galaxy" ], "tools": [ + "samtools_stats", + "fastq_to_fasta_python", + "gfastats", "porechop", "nanoplot", - "minimap2", - "samtools_stats", "fastqc", - "fastq_to_fasta_python", - "fasta_compute_length", - "gfastats" + "minimap2", + "fasta_compute_length" ], "update_time": "2024-12-12", "versions": 39 @@ -77210,16 +92482,16 @@ ], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "e97da2da9e0290a7", @@ -77235,22 +92507,22 @@ ], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2024-12-12", "versions": 1 @@ -77279,12 +92551,12 @@ "vgp" ], "tools": [ + "meryl_histogram_kmers", + "meryl_groups_kmers", "meryl_count_kmers", "meryl", - "pick_value", - "meryl_groups_kmers", "genomescope", - "meryl_histogram_kmers" + "pick_value" ], "update_time": "2024-12-12", "versions": 1 @@ -77313,11 +92585,11 @@ "vgp" ], "tools": [ - "meryl_count_kmers", - "pick_value", + "meryl_histogram_kmers", "meryl_groups_kmers", + "meryl_count_kmers", "genomescope", - "meryl_histogram_kmers" + "pick_value" ], "update_time": "2024-12-12", "versions": 1 @@ -77327,17 +92599,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "06d6dcd2655592af", @@ -77351,18 +92623,18 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_depth", - "samtools_flagstat", - "picard_MarkDuplicates", + "freebayes", + "snpEff", + "samtools_idxstats", "trimmomatic", "vcffilter2", "snpsift_vartype", - "snpEff", - "freebayes", + "samtools_depth", + "bwa_mem", "fastqc", "bamFilter", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-12-10", "versions": 0 @@ -77372,17 +92644,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "8daa91d54040ba95", @@ -77396,16 +92668,16 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_depth", - "samtools_flagstat", - "picard_MarkDuplicates", + "freebayes", + "samtools_idxstats", "trimmomatic", "vcffilter2", - "freebayes", + "samtools_depth", + "bwa_mem", "fastqc", "bamFilter", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-12-10", "versions": 2 @@ -77417,15 +92689,15 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "4dbac8374419d29e", @@ -77438,20 +92710,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", - "bwa_mem", - "picard_MarkDuplicates", + "freebayes", + "snpEff", "trimmomatic", - "tp_awk_tool", + "tp_tail_tool", "Cut1", - "tp_grep_tool", "tp_sed_tool", - "snpEff", - "freebayes", "bcftools_reheader", + "bwa_mem", "fastqc", "vcf2tsv", - "tp_tail_tool" + "tp_easyjoin_tool", + "tp_grep_tool", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-12-06", "versions": 14 @@ -77461,9 +92733,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", "Differential gene expression analysis", - "Gene functional annotation" + "Gene functional annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "420a332da24fb9e9", @@ -77476,13 +92748,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", + "goseq", "volcanoplot", - "Cut1", - "join1", - "Filter1", "interactive_tool_jupyter_notebook", - "goseq", + "join1", + "Cut1", "deseq2" ], "update_time": "2024-12-05", @@ -77496,20 +92768,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "a8e0f77cd6ef49f9", @@ -77525,25 +92797,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -77556,20 +92828,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "c983ea8a32662cd6", @@ -77585,25 +92857,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -77615,19 +92887,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "5d1208bd49f97aeb", @@ -77642,27 +92914,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -77672,8 +92944,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "34f706b7d4e61f44", @@ -77702,8 +92974,8 @@ "doi": "", "edam_operation": [ "Genome visualisation", - "Pathway visualisation", - "Structure visualisation" + "Structure visualisation", + "Pathway visualisation" ], "edam_topic": [], "id": "505c826e8c99d7bf", @@ -77716,15 +92988,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", + "tp_replace_in_line", + "deeptools_bigwig_compare", + "jbrowse2", "filter_by_fasta_ids", + "tp_easyjoin_tool", "Cut1", - "tp_replace_in_line", "pick_value", - "deeptools_bigwig_compare", - "fasta_compute_length", - "jbrowse2" + "fasta_compute_length" ], "update_time": "2024-12-02", "versions": 25 @@ -77734,16 +93006,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8041fad92ef6e904", @@ -77756,21 +93028,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-11-29", "versions": 0 @@ -77795,17 +93067,17 @@ "name:clinicalmp" ], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2024-11-28", "versions": 1 @@ -77833,8 +93105,8 @@ "name:clinicalmp" ], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2024-11-28", @@ -77847,10 +93119,10 @@ ], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -77894,16 +93166,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "decoupler_pseudobulk", - "volcanoplot", - "edger", - "column_remove_by_header", - "tp_awk_tool", "collection_element_identifiers", "param_value_from_file", + "edger", + "column_remove_by_header", "tp_replace_in_line", "split_file_to_collection", - "tp_replace_in_column" + "volcanoplot", + "tp_replace_in_column", + "decoupler_pseudobulk", + "tp_awk_tool" ], "update_time": "2024-11-28", "versions": 1 @@ -77915,8 +93187,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "25cdc47baba556c5", @@ -77932,20 +93204,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-28", "versions": 1 @@ -77958,10 +93230,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -77976,10 +93248,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-11-28", "versions": 1 @@ -78034,24 +93306,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-11-28", "versions": 1 @@ -78066,14 +93338,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "1be5c982c2d36a6c", @@ -78095,12 +93367,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-11-28", "versions": 1 @@ -78115,12 +93387,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "9e5c5ddb60a24889", @@ -78141,13 +93413,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-11-28", "versions": 1 @@ -78160,10 +93432,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78178,8 +93450,8 @@ "tags": [], "tools": [ "qiime2__metadata__tabulate", - "qiime2__dada2__denoise_paired", "qiime2__feature_table__tabulate_seqs", + "qiime2__dada2__denoise_paired", "qiime2__feature_table__summarize" ], "update_time": "2024-11-28", @@ -78193,10 +93465,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78226,10 +93498,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78245,8 +93517,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-11-28", @@ -78260,10 +93532,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78279,8 +93551,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-11-28", @@ -78294,10 +93566,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78312,8 +93584,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_paired", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-11-28", "versions": 1 @@ -78326,10 +93598,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -78344,8 +93616,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-11-28", "versions": 1 @@ -78358,14 +93630,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "42bc3a770f0ab6b8", @@ -78381,15 +93653,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-28", "versions": 1 @@ -78402,14 +93674,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "e55ca98817c1855e", @@ -78425,13 +93697,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-28", @@ -78445,14 +93717,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "2125db88b4a71c09", @@ -78468,13 +93740,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-28", @@ -78503,13 +93775,13 @@ ], "tools": [ "arriba_get_filters", - "rna_star", - "tp_awk_tool", - "tab2fasta", "regex1", + "tab2fasta", "arriba", + "CONVERTER_gz_to_uncompressed", + "rna_star", "query_tabular", - "CONVERTER_gz_to_uncompressed" + "tp_awk_tool" ], "update_time": "2024-11-27", "versions": 2 @@ -78537,11 +93809,11 @@ "mlmodel" ], "tools": [ + "sklearn_searchcv", "sklearn_build_pipeline", "sklearn_ensemble", - "Remove beginning1", - "sklearn_searchcv", - "plotly_ml_performance_plots" + "plotly_ml_performance_plots", + "Remove beginning1" ], "update_time": "2024-11-25", "versions": 4 @@ -78553,8 +93825,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "4c840284d2984fa0", @@ -78570,20 +93842,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-21", "versions": 1 @@ -78595,10 +93867,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "d47cddc372c88094", @@ -78612,12 +93884,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-11-21", "versions": 1 @@ -78630,14 +93902,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3ad9cdcda44b7dfb", @@ -78653,15 +93925,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-21", "versions": 1 @@ -78671,8 +93943,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ce99c56e45d982cb", @@ -78685,8 +93957,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deseq2", - "__TAG_FROM_FILE__" + "__TAG_FROM_FILE__", + "deseq2" ], "update_time": "2024-11-20", "versions": 1 @@ -78696,9 +93968,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "26b2057a8bc0386c", @@ -78711,8 +93983,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-11-15", "versions": 0 @@ -78725,14 +93997,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "8bcab83874cbc75c", @@ -78748,15 +94020,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-14", "versions": 1 @@ -78779,14 +94051,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rxdock_sort_filter", - "fpocket", - "cat_multiple", - "ctb_im_standardize", "prepare_receptor", - "__FLATTEN__", "prepare_box", - "docking" + "cat_multiple", + "docking", + "__FLATTEN__", + "rxdock_sort_filter", + "ctb_im_standardize", + "fpocket" ], "update_time": "2024-11-12", "versions": 4 @@ -78799,18 +94071,18 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Sequence contamination filtering", + "Statistical calculation", + "Genome assembly", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Variant calling", - "Genome assembly", - "Sequence contamination filtering", "Read pre-processing", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "71f8a4090877f171", @@ -78823,18 +94095,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_depth", - "picard_MarkDuplicates", - "trimmomatic", "bcftools_consensus", - "bcftools_call", "samtools_stats", + "trimmomatic", "ngsutils_bam_filter", - "fastqc", + "bcftools_call", "spades", + "bcftools_view", + "samtools_depth", + "bwa_mem", + "fastqc", "bcftools_mpileup", - "bcftools_view" + "picard_MarkDuplicates" ], "update_time": "2024-11-08", "versions": 23 @@ -78885,12 +94157,12 @@ "name:neoantigen" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", + "fragpipe", "collapse_dataset", - "validate_fasta_database", "query_tabular", - "fragpipe", - "Grep1" + "validate_fasta_database", + "Grep1", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2024-11-06", "versions": 1 @@ -78916,13 +94188,13 @@ "name:neoantigen" ], "tools": [ + "Filter1", "pepquery2", "table_compute", - "Cut1", "Remove beginning1", - "query_tabular", "iedb_api", - "Filter1" + "query_tabular", + "Cut1" ], "update_time": "2024-11-06", "versions": 1 @@ -78951,10 +94223,10 @@ "name:neoantigen" ], "tools": [ - "tp_awk_tool", "query_tabular", - "optitype", - "seq2hla" + "seq2hla", + "tp_awk_tool", + "optitype" ], "update_time": "2024-11-06", "versions": 1 @@ -78979,11 +94251,11 @@ "name:neoantigen" ], "tools": [ - "pep_pointer", "regexColumn1", "tab2fasta", - "query_tabular", - "Convert characters1" + "Convert characters1", + "pep_pointer", + "query_tabular" ], "update_time": "2024-11-06", "versions": 1 @@ -79012,9 +94284,9 @@ ], "tools": [ "msconvert", - "pepquery2", "tab2fasta", "ncbi_blastp_wrapper", + "pepquery2", "query_tabular" ], "update_time": "2024-11-06", @@ -79027,12 +94299,12 @@ ], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6a3e47124e32e260", @@ -79047,21 +94319,21 @@ "name:neoantigen" ], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", - "filter_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "CONVERTER_gz_to_uncompressed", - "custom_pro_db", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "gffcompare", + "stringtie", + "hisat2", + "bed_to_protein_map", + "custom_pro_db" ], "update_time": "2024-11-06", "versions": 1 @@ -79073,21 +94345,21 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Base-calling", - "De-novo assembly", + "Sequence contamination filtering", + "Statistical calculation", + "Genome assembly", "Sequence assembly", - "Sequence composition calculation", + "Mapping assembly", "Sequencing quality control", + "Base-calling", "Formatting", - "Variant calling", + "Cross-assembly", "Pairwise sequence alignment", - "Sequence contamination filtering", + "De-novo assembly", "Read pre-processing", - "Genome assembly", - "Statistical calculation", - "Mapping assembly", - "Cross-assembly" + "Sequence composition calculation", + "Variant calling", + "Filtering" ], "edam_topic": [], "id": "2ded909e7e3a9962", @@ -79100,20 +94372,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_depth", - "picard_MarkDuplicates", - "flye", - "porechop", "bcftools_consensus", - "filtlong", - "medaka_consensus", - "bcftools_call", - "minimap2", + "flye", "ngsutils_bam_filter", + "bcftools_call", + "medaka_consensus", + "porechop", + "samtools_depth", + "ivar_variants", + "bcftools_view", "fastqc", "bcftools_mpileup", - "ivar_variants", - "bcftools_view" + "filtlong", + "minimap2", + "picard_MarkDuplicates" ], "update_time": "2024-11-06", "versions": 20 @@ -79125,13 +94397,13 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", - "Read mapping", + "Statistical calculation", "Read pre-processing", "Sequence trimming", - "Sequencing quality control" + "Primer removal", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "fd30cdfe7e38b508", @@ -79149,8 +94421,8 @@ "bowtie2", "__EXTRACT_DATASET__", "trimmomatic", - "fastqc", "__BUILD_LIST__", + "fastqc", "cutadapt" ], "update_time": "2024-11-05", @@ -79163,18 +94435,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Sequence trimming", - "Genome indexing", "Statistical calculation", + "Sequence alignment", "Primer removal", - "Read pre-processing", + "Sequencing quality control", "Sequence file editing", - "Generation" + "Generation", + "Genome indexing", + "Sequence composition calculation", + "Read pre-processing", + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "3269026bb1e0ec42", @@ -79188,18 +94460,18 @@ "tags": [], "tools": [ "cat1", - "bwa_mem", + "Filter1", "seqtk_sample", - "bedtools_bamtofastq", - "trimmer", - "tp_replace_in_line", "seqtk_fqchk", - "fastqc", "tp_head_tool", - "Filter1", + "tp_replace_in_line", + "bam_to_sam", + "bedtools_bamtofastq", "sam_to_bam", + "bwa_mem", + "fastqc", "cutadapt", - "bam_to_sam" + "trimmer" ], "update_time": "2024-11-05", "versions": 10 @@ -79209,20 +94481,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome alignment", - "Data handling", - "Sequence assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", "Gene prediction", "Genome annotation", "Statistical calculation", + "Genome assembly", + "Sequence assembly", + "Sequencing quality control", "Sequence file editing", - "Taxonomic classification", "Query and retrieval", "Coding region prediction", - "Sequence analysis" + "Sequence composition calculation", + "Sequence analysis", + "Genome alignment", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "33d90e718ce500ef", @@ -79235,19 +94507,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cat_prepare", + "prokka", "trimmomatic", - "kraken", - "maxbin2", - "PlasFlow", "cat_contigs", - "metaspades", + "PlasFlow", + "cat_bins", + "cat_prepare", + "gtdbtk_classify_wf", + "seqtk_mergepe", "kraken-report", - "prokka", + "metaspades", "fastqc", - "seqtk_mergepe", - "cat_bins", - "gtdbtk_classify_wf" + "maxbin2", + "kraken" ], "update_time": "2024-11-04", "versions": 12 @@ -79300,9 +94572,9 @@ "bedtools" ], "tools": [ - "cshl_fasta_formatter", "tp_sed_tool", - "bedtools_getfastabed" + "bedtools_getfastabed", + "cshl_fasta_formatter" ], "update_time": "2024-11-01", "versions": 3 @@ -79314,14 +94586,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "ffae9c47980a5170", @@ -79338,19 +94610,19 @@ "haploid" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "collapse_dataset", - "tp_awk_tool", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "fastp", + "multiqc", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-10-31", "versions": 1 @@ -79383,24 +94655,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-10-31", "versions": 1 @@ -79415,16 +94687,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "4f8bdd61c524b901", @@ -79444,12 +94716,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-31", "versions": 1 @@ -79464,14 +94736,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "623fc80c7f91a33a", @@ -79493,12 +94765,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-31", "versions": 1 @@ -79513,12 +94785,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "c454c930ccfb0d3f", @@ -79539,13 +94811,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-10-31", "versions": 1 @@ -79561,8 +94833,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "2078a54de1f2628d", @@ -79586,10 +94858,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-31", "versions": 1 @@ -79601,10 +94873,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "a8e39acc103c3d6b", @@ -79618,12 +94890,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-10-31", "versions": 1 @@ -79635,13 +94907,13 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "3edd2957ecd26d6c", @@ -79661,13 +94933,13 @@ "metams" ], "tools": [ - "xcms_merge", "metams_runGC", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "checkFormat", "xcms_plot_chromatogram", - "Multivariate" + "msnbase_readmsdata", + "checkFormat", + "Multivariate", + "xcms_merge" ], "update_time": "2024-10-31", "versions": 1 @@ -79677,11 +94949,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", "Genome annotation", + "Genome assembly", "Sequence assembly validation", "Scaffolding", - "Genome assembly", + "Data handling", "Transcriptome assembly" ], "edam_topic": [], @@ -79709,14 +94981,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "7d6617b8316cee19", @@ -79733,19 +95005,19 @@ "haploid" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "collapse_dataset", - "tp_awk_tool", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "fastp", + "multiqc", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-10-29", "versions": 23 @@ -79768,12 +95040,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_sort_header_tool", - "comp1", - "datamash_ops", "Show beginning1", + "tp_tail_tool", "bedtools_intersectbed", - "tp_tail_tool" + "tp_sort_header_tool", + "comp1", + "datamash_ops" ], "update_time": "2024-10-29", "versions": 4 @@ -79796,12 +95068,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_sort_header_tool", - "comp1", - "datamash_ops", "Show beginning1", + "tp_tail_tool", "bedtools_intersectbed", - "tp_tail_tool" + "tp_sort_header_tool", + "comp1", + "datamash_ops" ], "update_time": "2024-10-29", "versions": 3 @@ -79811,9 +95083,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "bb2ac86b0440ae86", @@ -79826,9 +95098,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "hisat2", "samtool_filter2", - "featurecounts", - "hisat2" + "featurecounts" ], "update_time": "2024-10-23", "versions": 7 @@ -79853,8 +95125,8 @@ "halfdeep" ], "tools": [ - "samtools_sort", "minimap2", + "samtools_sort", "samtools_merge" ], "update_time": "2024-10-21", @@ -79871,8 +95143,8 @@ "doi": "", "edam_operation": [ "Genome visualisation", - "Pathway visualisation", - "Structure visualisation" + "Structure visualisation", + "Pathway visualisation" ], "edam_topic": [], "id": "386d3b300cf05305", @@ -79885,14 +95157,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", + "deeptools_bigwig_compare", + "jbrowse2", "filter_by_fasta_ids", + "tp_easyjoin_tool", "Cut1", "pick_value", - "deeptools_bigwig_compare", - "fasta_compute_length", - "jbrowse2" + "fasta_compute_length" ], "update_time": "2024-10-17", "versions": 45 @@ -79907,16 +95179,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "d2a5f6a5181aada5", @@ -79936,12 +95208,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-17", "versions": 1 @@ -79969,9 +95241,9 @@ "tags": [], "tools": [ "map_param_value", - "brew3r_r", "stringtie", - "stringtie_merge" + "stringtie_merge", + "brew3r_r" ], "update_time": "2024-10-17", "versions": 1 @@ -79986,14 +95258,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "b6a795834009ce06", @@ -80015,12 +95287,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-17", "versions": 1 @@ -80036,8 +95308,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "aaf8e740b3f8e2c0", @@ -80061,10 +95333,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-17", "versions": 1 @@ -80125,8 +95397,8 @@ "doi": "", "edam_operation": [ "Genome visualisation", - "Pathway visualisation", - "Structure visualisation" + "Structure visualisation", + "Pathway visualisation" ], "edam_topic": [], "id": "89d3c800d3be6050", @@ -80139,12 +95411,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", + "jbrowse2", "filter_by_fasta_ids", + "tp_easyjoin_tool", "Cut1", - "fasta_compute_length", - "jbrowse2" + "fasta_compute_length" ], "update_time": "2024-10-09", "versions": 26 @@ -80156,8 +95428,8 @@ ], "doi": "", "edam_operation": [ - "Mapping", - "Genome annotation" + "Genome annotation", + "Mapping" ], "edam_topic": [], "id": "f2f633d2b02b6050", @@ -80171,13 +95443,13 @@ "tags": [], "tools": [ "__EXTRACT_DATASET__", - "tp_grep_tool", "cat_multiple", - "pick_value", "repeatmasker_wrapper", - "bedtools_sortbed", + "tp_cat", "split_file_to_collection", - "tp_cat" + "bedtools_sortbed", + "tp_grep_tool", + "pick_value" ], "update_time": "2024-10-05", "versions": 3 @@ -80250,14 +95522,14 @@ ], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "2404d5e5b1817825", @@ -80272,8 +95544,8 @@ "name:clinicalmp" ], "tools": [ - "Cut1", "Grep1", + "Cut1", "Grouping1", "maxquant" ], @@ -80290,16 +95562,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "993534c11310a207", @@ -80319,12 +95591,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-10-03", "versions": 1 @@ -80339,14 +95611,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Expression analysis", + "Parsing", "Sequencing quality control", - "Statistical calculation", - "Sequence contamination filtering", - "Taxonomic classification", "Cross-assembly", - "Parsing" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "9f68718f025bed30", @@ -80368,12 +95640,12 @@ "trimming" ], "tools": [ - "tooldistillator_summarize", + "recentrifuge", "kraken2", - "est_abundance", "fastp", "tooldistillator", - "recentrifuge" + "est_abundance", + "tooldistillator_summarize" ], "update_time": "2024-10-03", "versions": 1 @@ -80388,12 +95660,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "9ac1e4efe310b3b3", @@ -80414,13 +95686,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-10-03", "versions": 1 @@ -80436,8 +95708,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "ef187f85b103d858", @@ -80461,10 +95733,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-10-03", "versions": 1 @@ -80490,20 +95762,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-10-03", "versions": 1 @@ -80515,14 +95787,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "7e2651e5ed17e3db", @@ -80539,26 +95811,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-10-03", "versions": 1 @@ -80594,23 +95866,23 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", "DNA mapping", - "Chimera detection", - "Sequence merging", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Genome assembly", - "Sequence alignment", - "Read binning", - "Visualisation", "Sequence contamination filtering", + "Visualisation", "Statistical calculation", + "Genome assembly", + "Read binning", + "Sequence alignment", + "Chimera detection", + "Sequencing quality control", + "Sequence trimming", + "Aggregation", + "Sequence composition calculation", "Taxonomic classification", "RNA-Seq analysis", - "Sequence trimming" + "Read mapping", + "Data handling", + "Sequence merging" ], "edam_topic": [], "id": "0a61de91bbbe02ad", @@ -80623,22 +95895,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bbtools_bbmap", - "ncbi_blastx_wrapper", + "krakentools_extract_kraken_reads", "fastq_groomer", - "trimmomatic", + "__DUPLICATE_FILE_TO_COLLECTION__", "kraken2", + "trimmomatic", + "spades_rnaviralspades", + "ncbi_blastx_wrapper", + "blastxml_to_tabular", "bedtools_bamtofastq", - "fastq_dump", "fastq_info", - "vsearch_clustering", - "krakentools_extract_kraken_reads", - "tp_grep_tool", - "blastxml_to_tabular", "iuc_pear", "fastqc", - "__DUPLICATE_FILE_TO_COLLECTION__", - "spades_rnaviralspades" + "tp_grep_tool", + "fastq_dump", + "vsearch_clustering", + "bbtools_bbmap" ], "update_time": "2024-09-30", "versions": 58 @@ -80652,9 +95924,9 @@ ], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", "Coding region prediction", + "Genome visualisation", "Genome annotation" ], "edam_topic": [], @@ -80671,8 +95943,8 @@ "gtn" ], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2024-09-27", "versions": 0 @@ -80687,16 +95959,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "04c5ea133de3204c", @@ -80716,12 +95988,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-26", "versions": 1 @@ -80736,16 +96008,16 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Data handling", - "Nucleic acid feature detection", - "Multilocus sequence typing", "Genome annotation", "Sequence motif recognition", + "Genome assembly", + "Multilocus sequence typing", + "Parsing", "Scaffolding", + "Protein feature detection", "Structural variation detection", - "Genome assembly", - "Parsing" + "Nucleic acid feature detection", + "Data handling" ], "edam_topic": [], "id": "8cb8a588a0495cfa", @@ -80765,12 +96037,12 @@ "genome-annotation" ], "tools": [ - "tooldistillator_summarize", "bakta", - "integron_finder", - "plasmidfinder", + "tooldistillator_summarize", + "tooldistillator", "isescan", - "tooldistillator" + "integron_finder", + "plasmidfinder" ], "update_time": "2024-09-26", "versions": 1 @@ -80785,12 +96057,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "4d1279007d0137fa", @@ -80811,13 +96083,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-26", "versions": 1 @@ -80833,8 +96105,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "3c177fdf38311118", @@ -80858,10 +96130,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-26", "versions": 1 @@ -80877,11 +96149,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "516a2181b41af94e", @@ -80929,9 +96201,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-26", "versions": 1 @@ -80945,10 +96217,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "31ed5a2bcc8da51a", @@ -80963,24 +96235,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -80994,10 +96266,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "56427a9b9c3848bf", @@ -81012,23 +96284,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -81042,10 +96314,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "affdc1bf42475cc9", @@ -81060,23 +96332,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-26", "versions": 1 @@ -81088,14 +96360,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "89f52c97b3aee938", @@ -81110,14 +96382,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -81129,14 +96401,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1234a128adc25b03", @@ -81151,14 +96423,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -81170,15 +96442,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c69f8c26ec5fb8a6", @@ -81193,13 +96465,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -81211,19 +96483,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "7c4a2339b17a8930", @@ -81238,27 +96510,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -81270,15 +96542,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "df8b49863e83824d", @@ -81293,13 +96565,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -81311,17 +96583,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fce1837144d3a86e", @@ -81336,15 +96608,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-26", "versions": 1 @@ -81357,10 +96629,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -81375,10 +96647,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-09-19", "versions": 1 @@ -81414,9 +96686,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "4b5f6b5d4f36e38b", @@ -81434,8 +96706,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-09-19", @@ -81452,12 +96724,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "3ef08553982f6ffc", @@ -81475,28 +96747,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-09-19", "versions": 1 @@ -81510,15 +96782,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "3f252e077e0bcce5", @@ -81536,18 +96808,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-09-19", "versions": 1 @@ -81560,8 +96832,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "450c2181f89e6b23", @@ -81574,18 +96846,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -81598,8 +96870,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "f18e6fa5270fcd37", @@ -81612,18 +96884,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -81651,9 +96923,9 @@ "tags": [], "tools": [ "map_param_value", - "brew3r_r", "stringtie", - "stringtie_merge" + "stringtie_merge", + "brew3r_r" ], "update_time": "2024-09-19", "versions": 1 @@ -81668,12 +96940,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "f4d623a19b32370e", @@ -81694,13 +96966,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -81715,12 +96987,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "0e30324072570abb", @@ -81741,13 +97013,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -81762,12 +97034,12 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence assembly validation", - "Parsing", "Visualisation", "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequence assembly validation", + "Parsing", + "Data handling" ], "edam_topic": [], "id": "4161cfd67ed94b5d", @@ -81788,13 +97060,13 @@ "abromics" ], "tools": [ - "refseq_masher_matches", - "tooldistillator_summarize", + "bandage_info", "bandage_image", "quast", - "shovill", "tooldistillator", - "bandage_info" + "tooldistillator_summarize", + "refseq_masher_matches", + "shovill" ], "update_time": "2024-09-19", "versions": 1 @@ -81810,8 +97082,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "fde774a049875466", @@ -81835,10 +97107,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-19", "versions": 1 @@ -81854,8 +97126,8 @@ "doi": "", "edam_operation": [ "Data handling", - "Antimicrobial resistance prediction", - "Parsing" + "Parsing", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "2b4b1fe82258f303", @@ -81879,10 +97151,10 @@ ], "tools": [ "abricate", + "tooldistillator", "tooldistillator_summarize", - "staramr_search", "amrfinderplus", - "tooldistillator" + "staramr_search" ], "update_time": "2024-09-19", "versions": 1 @@ -81895,10 +97167,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -81913,8 +97185,8 @@ "tags": [], "tools": [ "qiime2__metadata__tabulate", - "qiime2__dada2__denoise_paired", "qiime2__feature_table__tabulate_seqs", + "qiime2__dada2__denoise_paired", "qiime2__feature_table__summarize" ], "update_time": "2024-09-19", @@ -81928,10 +97200,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -81961,10 +97233,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -81980,8 +97252,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -81995,10 +97267,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -82014,8 +97286,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -82029,10 +97301,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -82047,8 +97319,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_paired", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -82061,10 +97333,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -82079,8 +97351,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -82093,8 +97365,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "78e60413358273bc", @@ -82109,17 +97381,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-09-19", "versions": 1 @@ -82132,16 +97404,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "6fc7497c86ebd8ee", @@ -82156,17 +97428,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82179,16 +97451,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "242ef2e9dee35702", @@ -82203,17 +97475,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82226,16 +97498,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "7adf904dea83e699", @@ -82250,20 +97522,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82276,16 +97548,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "cb4ccd3068819418", @@ -82300,20 +97572,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82344,9 +97616,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-19", "versions": 1 @@ -82358,13 +97630,13 @@ ], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "aeeaf3e06a13bc22", @@ -82384,15 +97656,15 @@ "gtn" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", "intens_check", - "xcms_plot_chromatogram", + "abims_xcms_xcmsSet", "abims_xcms_retcor", - "abims_xcms_group" + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport" ], "update_time": "2024-09-19", "versions": 1 @@ -82421,14 +97693,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -82456,17 +97728,17 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", - "gfastats", - "Cut1", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_sed_tool", "tp_grep_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "tp_cat", + "gfastats", + "tp_sed_tool", + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -82494,15 +97766,15 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", + "ncbi_blastn_wrapper", + "tp_cat", "gfastats", - "Cut1", "tp_sed_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -82516,20 +97788,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f1a54b10d4afce8f", @@ -82545,23 +97817,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82575,20 +97847,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9938a81fb6911412", @@ -82604,23 +97876,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82634,20 +97906,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fd40e50c9f1545ce", @@ -82663,23 +97935,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82693,20 +97965,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9ddfdc9d6cacea88", @@ -82722,26 +97994,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82755,20 +98027,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "484f8fcf21d67376", @@ -82784,26 +98056,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82817,20 +98089,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "07e873a6d75dfe9f", @@ -82846,26 +98118,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82878,20 +98150,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3f7550d5d2bf0b96", @@ -82907,22 +98179,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82935,20 +98207,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "305fb9f84b053713", @@ -82964,22 +98236,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -82992,20 +98264,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "284150bb1f296378", @@ -83021,22 +98293,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83049,20 +98321,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fa26fd51caea53c7", @@ -83078,25 +98350,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83109,8 +98381,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "d5183b025d0e78dd", @@ -83125,11 +98397,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -83142,8 +98414,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "b1cfa3c239ef2523", @@ -83158,12 +98430,12 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", - "tp_find_and_replace", "param_value_from_file", - "gfastats" + "tp_find_and_replace", + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -83190,8 +98462,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -83218,8 +98490,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -83246,8 +98518,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -83260,16 +98532,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "cc50da71cdf6f244", @@ -83285,16 +98557,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83307,16 +98579,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "426358bd988cb39d", @@ -83332,16 +98604,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83354,16 +98626,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9ab68c65337b893b", @@ -83379,20 +98651,20 @@ ], "tools": [ "cat1", + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "merqury", "gfastats", - "Cut1", - "tp_awk_tool", + "busco", "join1", - "param_value_from_file", "tp_cut_tool", - "tp_find_and_replace", "minimap2", - "merqury", - "compose_text_param", - "busco", - "purge_dups" + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83405,13 +98677,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83427,19 +98699,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83452,13 +98724,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83474,19 +98746,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83499,13 +98771,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83521,20 +98793,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83547,13 +98819,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83569,20 +98841,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83595,13 +98867,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83617,20 +98889,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83643,13 +98915,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -83665,21 +98937,21 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "compose_text_param", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -83706,15 +98978,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", "versions": 1 @@ -83741,15 +99013,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", "versions": 1 @@ -83776,15 +99048,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", "versions": 1 @@ -83811,15 +99083,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", "versions": 1 @@ -83832,8 +99104,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "e3366346808b1f55", @@ -83846,8 +99118,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -83860,8 +99132,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "84112c29ee53a5db", @@ -83888,19 +99160,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "8d605fbd33003d26", @@ -83916,21 +99188,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83943,19 +99215,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1d24cc949c52e475", @@ -83971,21 +99243,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -83998,19 +99270,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "bfef75672b9c3ea4", @@ -84026,21 +99298,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84053,20 +99325,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "ab0be4897d5355ac", @@ -84082,25 +99354,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84113,20 +99385,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "7072731b51e16923", @@ -84142,25 +99414,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84183,14 +99455,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2024-09-19", "versions": 1 @@ -84204,10 +99476,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5c85cd8c56b9f6ab", @@ -84222,20 +99494,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -84249,10 +99521,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d02b4d7483936b73", @@ -84267,24 +99539,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84298,10 +99570,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "305eafecadfa8815", @@ -84316,24 +99588,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84347,10 +99619,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6f2e4b4860413153", @@ -84365,19 +99637,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84391,10 +99663,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b7ec8d79dc563a93", @@ -84409,19 +99681,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84435,10 +99707,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e325b97b81b10edb", @@ -84453,23 +99725,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84483,10 +99755,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "931dd3e6b1fae4f5", @@ -84501,23 +99773,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84531,10 +99803,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "97dcd7285ebd5817", @@ -84549,19 +99821,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84575,10 +99847,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "462a1176b48eef4a", @@ -84593,19 +99865,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84619,10 +99891,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ebe7f93204402a5a", @@ -84637,23 +99909,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84667,10 +99939,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "170287dcfb9de475", @@ -84685,23 +99957,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-09-19", "versions": 1 @@ -84713,14 +99985,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3ab66315f50501f0", @@ -84735,14 +100007,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84754,14 +100026,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "87eb1a8ee7a2c984", @@ -84776,14 +100048,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84795,14 +100067,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3e57e668cf698d19", @@ -84817,14 +100089,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84836,14 +100108,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "bd2ce9a97c1598df", @@ -84858,14 +100130,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84877,15 +100149,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "27ee9da9121d0522", @@ -84900,13 +100172,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84918,15 +100190,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "bae2d6b436cd80ef", @@ -84941,13 +100213,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -84959,15 +100231,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3c076bc8551a23d2", @@ -84982,13 +100254,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85000,15 +100272,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "824730064b5014e5", @@ -85023,13 +100295,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85041,19 +100313,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "3673a1ced343d0d0", @@ -85068,27 +100340,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85100,19 +100372,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "15ea806eaf077617", @@ -85127,27 +100399,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85159,19 +100431,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "336795e890851c21", @@ -85186,27 +100458,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85218,19 +100490,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "7b9e17cb1d72d7e4", @@ -85245,27 +100517,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85277,15 +100549,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ec66767cab0022ee", @@ -85300,13 +100572,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85318,15 +100590,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "66e6b41f6c6d52b7", @@ -85341,13 +100613,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85359,15 +100631,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "148c071f5c5a4586", @@ -85382,13 +100654,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85400,15 +100672,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9f1e8e82fb3e2033", @@ -85423,13 +100695,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -85441,17 +100713,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d2759906e4124964", @@ -85466,15 +100738,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -85486,17 +100758,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Mapping", - "Validation" + "Gene regulatory network analysis", + "Sequence trimming", + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "af71519c81429287", @@ -85511,15 +100783,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -85531,17 +100803,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "789647a199e563fd", @@ -85556,15 +100828,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -85576,17 +100848,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f765c8aa4bc3176c", @@ -85601,15 +100873,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -85636,8 +100908,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -85664,8 +100936,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -85677,15 +100949,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "5dd0a672cceb15ec", @@ -85700,13 +100972,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85718,15 +100990,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2f4d5f833aa1c981", @@ -85741,13 +101013,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85759,15 +101031,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c4ac09605633655c", @@ -85782,13 +101054,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85800,15 +101072,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "995cc428eace3bc4", @@ -85823,13 +101095,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85841,19 +101113,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "2957924403998f3a", @@ -85868,27 +101140,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85900,19 +101172,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "156e245e3d9f22ce", @@ -85927,27 +101199,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -85959,19 +101231,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "88e10493f7e6b9d5", @@ -85986,27 +101258,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86018,19 +101290,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "a99a938953be5fd6", @@ -86045,27 +101317,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86077,15 +101349,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1d69ab87c94d68fd", @@ -86100,13 +101372,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86118,15 +101390,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e9f4de639f4cfe02", @@ -86141,13 +101413,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86159,15 +101431,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "917e5a21d51a61ce", @@ -86182,13 +101454,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86200,15 +101472,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "5b8497a32bf01c4f", @@ -86223,13 +101495,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-12", "versions": 1 @@ -86241,17 +101513,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "533b1d5d08f9943e", @@ -86266,15 +101538,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-12", "versions": 1 @@ -86286,17 +101558,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c2898d28a3b380d6", @@ -86311,15 +101583,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-12", "versions": 1 @@ -86331,17 +101603,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b232caf4a1e1b7ee", @@ -86356,15 +101628,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-12", "versions": 1 @@ -86376,17 +101648,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c1ec12905944ca7b", @@ -86401,15 +101673,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-12", "versions": 1 @@ -86436,8 +101708,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-12", "versions": 1 @@ -86464,8 +101736,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-12", "versions": 1 @@ -86477,15 +101749,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a63d3ee4a2a4a20b", @@ -86500,13 +101772,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86518,15 +101790,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "acae55e8f37fea59", @@ -86541,13 +101813,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86559,15 +101831,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "444c856f03b6d2a7", @@ -86582,13 +101854,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86600,15 +101872,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f7975ae799daf463", @@ -86623,13 +101895,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86641,19 +101913,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "9255c0c9017b139f", @@ -86668,27 +101940,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86700,19 +101972,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "dcf658333596d76a", @@ -86727,27 +101999,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86759,19 +102031,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "b78a75ae89ae4c79", @@ -86786,27 +102058,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86818,19 +102090,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "13a1fa4f6daf65cc", @@ -86845,27 +102117,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86877,15 +102149,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "94ab68d27de2e60f", @@ -86900,13 +102172,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86918,15 +102190,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fb588edfd343b24d", @@ -86941,13 +102213,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -86959,15 +102231,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "bf3f71a748d88490", @@ -86982,13 +102254,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -87000,15 +102272,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ae1de4267e4da154", @@ -87023,13 +102295,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-05", "versions": 1 @@ -87041,17 +102313,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5ccc7d708e13de60", @@ -87066,15 +102338,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-05", "versions": 1 @@ -87086,17 +102358,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "edf9be785ab9eb65", @@ -87111,15 +102383,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-05", "versions": 1 @@ -87131,17 +102403,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "914ec4d8fc0022e4", @@ -87156,15 +102428,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-05", "versions": 1 @@ -87176,17 +102448,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fc130cb411aa7d06", @@ -87201,15 +102473,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-05", "versions": 1 @@ -87236,8 +102508,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-05", "versions": 1 @@ -87264,8 +102536,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-05", "versions": 1 @@ -87299,15 +102571,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f18946db4c93e88b", @@ -87322,13 +102594,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87340,15 +102612,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a8f633b79b20c760", @@ -87363,13 +102635,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87381,15 +102653,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "06b489dc859f6e39", @@ -87404,13 +102676,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87422,15 +102694,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ae5327f6f30b6138", @@ -87445,13 +102717,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87463,19 +102735,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "506acac8c6a58d5e", @@ -87490,27 +102762,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87522,19 +102794,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "e9ffad95baa43478", @@ -87549,27 +102821,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87581,19 +102853,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "60b9910b7bb69f47", @@ -87608,27 +102880,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87640,19 +102912,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "1ffc71df8eeed57e", @@ -87667,27 +102939,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87699,15 +102971,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "33e827d75a0074df", @@ -87722,13 +102994,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87740,15 +103012,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7df3246858cd83d1", @@ -87763,13 +103035,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87781,15 +103053,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "098fd236c5e2895d", @@ -87804,13 +103076,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87822,15 +103094,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "05e86b4df0d14800", @@ -87845,13 +103117,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-29", "versions": 1 @@ -87863,17 +103135,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d9840d6ecf2b4d2f", @@ -87888,15 +103160,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-29", "versions": 1 @@ -87908,17 +103180,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6c95a357a3c1f399", @@ -87933,15 +103205,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-29", "versions": 1 @@ -87953,17 +103225,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "672125473ec700bc", @@ -87978,15 +103250,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-29", "versions": 1 @@ -87998,17 +103270,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6c68072bf72e6c4a", @@ -88023,15 +103295,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-29", "versions": 1 @@ -88058,8 +103330,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-29", "versions": 1 @@ -88086,8 +103358,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-29", "versions": 1 @@ -88099,15 +103371,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "76fb573f1372ae86", @@ -88122,13 +103394,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88140,15 +103412,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f93b5864d6d2659c", @@ -88163,13 +103435,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88181,15 +103453,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9124c2ec80b35680", @@ -88204,13 +103476,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88222,15 +103494,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "10c5f3c5cadd7417", @@ -88245,13 +103517,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88263,19 +103535,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "8bf608c6fd0dabd0", @@ -88290,27 +103562,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88322,19 +103594,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "6db96a9c7e4b8d14", @@ -88349,27 +103621,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88381,19 +103653,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "cd5f803c80875b9c", @@ -88408,27 +103680,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88440,19 +103712,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "98a4b90f7fc2bfce", @@ -88467,27 +103739,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88499,15 +103771,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "028f1beead539975", @@ -88522,13 +103794,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88540,15 +103812,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "45cb3e98b1319c7c", @@ -88563,13 +103835,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88581,15 +103853,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8f392d06d32bdf14", @@ -88604,13 +103876,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88622,15 +103894,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "35c022174ce79c1e", @@ -88645,13 +103917,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-22", "versions": 1 @@ -88663,17 +103935,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f29d1bcfeaacba04", @@ -88688,15 +103960,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-22", "versions": 1 @@ -88708,17 +103980,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "172ee5e5bef33d2e", @@ -88733,15 +104005,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-22", "versions": 1 @@ -88753,17 +104025,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6229546fb8b0eba9", @@ -88778,15 +104050,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-22", "versions": 1 @@ -88798,17 +104070,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "bd3bed78eb99e294", @@ -88823,15 +104095,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-22", "versions": 1 @@ -88858,8 +104130,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-22", "versions": 1 @@ -88886,8 +104158,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-22", "versions": 1 @@ -88899,15 +104171,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a8e5adb65d064641", @@ -88922,13 +104194,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -88940,15 +104212,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3b2bee20f0cfd957", @@ -88963,13 +104235,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -88981,15 +104253,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8cbb9936e88d4f49", @@ -89004,13 +104276,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89022,15 +104294,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "62ecc8078a396e9e", @@ -89045,13 +104317,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89063,19 +104335,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "93cb976bd4ae546e", @@ -89090,27 +104362,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89122,19 +104394,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "527adadecbab2eb6", @@ -89149,27 +104421,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89181,19 +104453,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "553125cd799e5982", @@ -89208,27 +104480,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89240,19 +104512,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "1250ec3ad6199cda", @@ -89267,27 +104539,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", - "bamFilter", - "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", - "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", "multiqc", - "bowtie2", - "bedtools_coveragebed", + "bamFilter", "cutadapt", - "bedtools_mergebed" + "samtools_view", + "picard_MarkDuplicates", + "macs2_callpeak", + "cat1", + "bedtools_coveragebed", + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89299,15 +104571,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c30bfd545ef3a228", @@ -89322,13 +104594,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89340,15 +104612,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fcbd4767298488b9", @@ -89363,13 +104635,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89381,15 +104653,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ac87b6133de6a03f", @@ -89404,13 +104676,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89422,15 +104694,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3b5437544ca3b5dc", @@ -89445,13 +104717,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-15", "versions": 1 @@ -89463,17 +104735,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b19a9163c26f1270", @@ -89488,15 +104760,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-15", "versions": 1 @@ -89508,17 +104780,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f5bd2da36ab0a870", @@ -89533,15 +104805,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-15", "versions": 1 @@ -89553,17 +104825,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8e2b2a40831dfb08", @@ -89578,15 +104850,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-15", "versions": 1 @@ -89598,17 +104870,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "62c842e67fca5ab7", @@ -89623,15 +104895,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-15", "versions": 1 @@ -89658,8 +104930,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-15", "versions": 1 @@ -89686,8 +104958,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-15", "versions": 1 @@ -89711,13 +104983,13 @@ "tags": [], "tools": [ "arriba_get_filters", - "rna_star", - "tp_awk_tool", - "tab2fasta", "regex1", + "tab2fasta", "arriba", + "CONVERTER_gz_to_uncompressed", + "rna_star", "query_tabular", - "CONVERTER_gz_to_uncompressed" + "tp_awk_tool" ], "update_time": "2024-08-12", "versions": 0 @@ -89727,12 +104999,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "e336bca259abd474", @@ -89745,23 +105017,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "gffcompare", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", - "filter_tabular", "sqlite_to_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "CONVERTER_gz_to_uncompressed", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "stringtie", + "hisat2", + "bed_to_protein_map" ], "update_time": "2024-08-12", "versions": 1 @@ -89773,15 +105045,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1d56a0975fca0e99", @@ -89796,13 +105068,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -89814,15 +105086,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1e0a55635f5b04cf", @@ -89837,13 +105109,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -89855,15 +105127,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4612ec88a57ab9e7", @@ -89878,13 +105150,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -89896,15 +105168,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c0a108e53ab05b0d", @@ -89919,13 +105191,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -89937,19 +105209,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "adb86df9061dca2b", @@ -89964,27 +105236,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -89996,19 +105268,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "d903c7215a88c79f", @@ -90023,27 +105295,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90055,19 +105327,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "c81833a367445f98", @@ -90082,27 +105354,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90114,19 +105386,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "b1dc9cf054a63be5", @@ -90141,27 +105413,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90173,15 +105445,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "642e71c64a975461", @@ -90196,13 +105468,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90214,15 +105486,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "448a0797f9150198", @@ -90237,13 +105509,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90255,15 +105527,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "12a52ae52e0f1053", @@ -90278,13 +105550,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90296,15 +105568,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "52592de9687fc6de", @@ -90319,13 +105591,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-08", "versions": 1 @@ -90337,17 +105609,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4790266996f12979", @@ -90362,15 +105634,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-08", "versions": 1 @@ -90382,17 +105654,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c712b85a55da2a2d", @@ -90407,15 +105679,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-08", "versions": 1 @@ -90427,17 +105699,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "51d80a44d7d6fff7", @@ -90452,15 +105724,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-08", "versions": 1 @@ -90472,17 +105744,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9373050c3ce80d56", @@ -90497,15 +105769,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-08", "versions": 1 @@ -90532,8 +105804,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-08", "versions": 1 @@ -90560,8 +105832,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-08", "versions": 1 @@ -90573,15 +105845,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f1c2d920bd41cebb", @@ -90596,13 +105868,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90614,15 +105886,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "5e18bbbe9ff2d9f5", @@ -90637,13 +105909,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90655,15 +105927,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "761675cb2c9ad2ef", @@ -90678,13 +105950,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90696,15 +105968,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "87756e064ab1e28a", @@ -90719,13 +105991,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90737,19 +106009,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "a164d857439a126f", @@ -90764,27 +106036,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90796,19 +106068,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "f0ee8bcd7c8fadca", @@ -90823,27 +106095,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90855,19 +106127,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "ea4c2defce2f5258", @@ -90882,27 +106154,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90914,19 +106186,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "1e1d7fac7e241768", @@ -90941,27 +106213,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -90973,15 +106245,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ec2f77224324f22e", @@ -90996,13 +106268,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -91014,15 +106286,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "6dfe0c6e87c6cb7b", @@ -91037,13 +106309,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -91055,15 +106327,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "07dca0dc191fb1de", @@ -91078,13 +106350,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -91096,15 +106368,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "06f3ca70b542556e", @@ -91119,13 +106391,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-08-01", "versions": 1 @@ -91137,17 +106409,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fe4c2791508c56ab", @@ -91162,15 +106434,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-01", "versions": 1 @@ -91182,17 +106454,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "64a329cf75834d6b", @@ -91207,15 +106479,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-01", "versions": 1 @@ -91227,17 +106499,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fa226c044fa026ef", @@ -91252,15 +106524,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-01", "versions": 1 @@ -91272,17 +106544,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "87c1bdc00b975377", @@ -91297,15 +106569,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-08-01", "versions": 1 @@ -91332,8 +106604,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-01", "versions": 1 @@ -91360,8 +106632,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-08-01", "versions": 1 @@ -91382,9 +106654,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "snpSift_annotate", + "snpEff", "bcftools_view", - "snpEff" + "snpSift_annotate" ], "update_time": "2024-07-28", "versions": 0 @@ -91396,15 +106668,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ba5889301928907f", @@ -91419,13 +106691,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91437,15 +106709,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a17af8b7b2b39c1a", @@ -91460,13 +106732,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91478,15 +106750,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "85011076892808e0", @@ -91501,13 +106773,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91519,15 +106791,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "063173d36c254105", @@ -91542,13 +106814,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91560,19 +106832,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "ca36eebd59575df3", @@ -91587,27 +106859,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91619,19 +106891,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "472f73c3e81da1d9", @@ -91646,27 +106918,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91678,19 +106950,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "99ee567c092fb34c", @@ -91705,27 +106977,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91737,19 +107009,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "8095deba606ebd5e", @@ -91764,27 +107036,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91796,15 +107068,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "efe7ca87323773c0", @@ -91819,13 +107091,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91837,15 +107109,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e7fa48d7fd40908b", @@ -91860,13 +107132,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91878,15 +107150,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "92aab10842ff610d", @@ -91901,13 +107173,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91919,15 +107191,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "70f9c7cc75a1d3c0", @@ -91942,13 +107214,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-25", "versions": 1 @@ -91960,17 +107232,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5a55d9bd9701b1ce", @@ -91985,15 +107257,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-25", "versions": 1 @@ -92005,17 +107277,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "424acfc2ded46f9f", @@ -92030,15 +107302,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-25", "versions": 1 @@ -92050,17 +107322,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4a01263e3d4b4edb", @@ -92075,15 +107347,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-25", "versions": 1 @@ -92095,17 +107367,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9763787d7b102f39", @@ -92120,15 +107392,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-25", "versions": 1 @@ -92155,8 +107427,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-25", "versions": 1 @@ -92183,8 +107455,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-25", "versions": 1 @@ -92194,17 +107466,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "7022c4d9af725e5c", @@ -92217,16 +107489,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rseqc_read_distribution", + "rseqc_geneBody_coverage", "featurecounts", + "samtools_idxstats", + "cutadapt", + "multiqc", "fasterq_dump", "gtftobed12", - "hisat2", - "multiqc", - "rseqc_geneBody_coverage", "fastqc", - "samtools_idxstats", - "cutadapt" + "hisat2", + "rseqc_read_distribution" ], "update_time": "2024-07-24", "versions": 3 @@ -92238,26 +107510,26 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence merging", - "Sequence alignment analysis", - "De-novo assembly", - "Sequencing quality control", - "Data retrieval", - "Genome assembly", - "Genome indexing", - "Generation", + "Genome annotation", + "Sequence alignment", "Database search", - "Sequence composition calculation", - "Read mapping", + "Sequencing quality control", + "Transcriptome assembly", + "Coding region prediction", "Sequence database search", - "Sequence alignment", + "Read mapping", + "Sequence merging", "Gene prediction", - "Genome annotation", "Statistical calculation", - "Taxonomic classification", - "Coding region prediction", - "Transcriptome assembly" + "Genome assembly", + "Sequence composition calculation", + "De-novo assembly", + "Sequence alignment analysis", + "Generation", + "Genome indexing", + "Data retrieval", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "e1d2a3bdc900af09", @@ -92270,21 +107542,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "bg_diamond_makedb", - "trimmomatic", - "kraken2", - "bwa", - "fastq_dump", - "bedtools_bamtofastq", - "orfipy", "prokka", - "bg_diamond", + "kraken2", + "trimmomatic", "spades_rnaviralspades", + "bg_diamond", + "bedtools_bamtofastq", "iuc_pear", - "fastqc", "datasets_download_genome", - "bamtools_split_mapped" + "fastqc", + "orfipy", + "bamtools_split_mapped", + "bwa", + "fastq_dump", + "bg_diamond_makedb", + "fastq_groomer" ], "update_time": "2024-07-22", "versions": 66 @@ -92298,8 +107570,8 @@ "doi": "", "edam_operation": [ "Visualisation", - "Analysis", "Deposition", + "Analysis", "Variant calling", "DNA barcoding" ], @@ -92316,24 +107588,24 @@ "microbiome" ], "tools": [ + "dada2_makeSequenceTable", + "collection_element_identifiers", "cat1", + "dada2_assignTaxonomyAddspecies", "Add_a_column1", "dada2_plotQualityProfile", - "dada2_makeSequenceTable", - "phyloseq_from_dada2", - "collection_element_identifiers", + "dada2_dada", + "tp_head_tool", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "tp_replace_in_line", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", - "dada2_learnErrors", + "tp_replace_in_line", "__SORTLIST__", - "dada2_dada", - "tp_head_tool", + "dada2_learnErrors", + "dada2_mergePairs", "tp_replace_in_column", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "phyloseq_from_dada2", + "__UNZIP_COLLECTION__" ], "update_time": "2024-07-19", "versions": 0 @@ -92345,15 +107617,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8e918c12d2f0d1fc", @@ -92368,13 +107640,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92386,15 +107658,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "adbed5c956a71543", @@ -92409,13 +107681,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92427,15 +107699,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b86d24a103181742", @@ -92450,13 +107722,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92468,15 +107740,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9c688a2fc8d1bf4e", @@ -92491,13 +107763,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92509,19 +107781,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "91806144e90637e8", @@ -92536,27 +107808,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92568,19 +107840,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "2b5346b94358df88", @@ -92595,27 +107867,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92627,19 +107899,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "00bc4e99626da1ba", @@ -92654,27 +107926,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92686,19 +107958,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "cbbd7e95041d9429", @@ -92713,27 +107985,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92745,15 +108017,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4b7daa3c73c8ef30", @@ -92768,13 +108040,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92786,15 +108058,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1cbd946c4cc0e7b9", @@ -92809,13 +108081,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92827,15 +108099,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9da9ddae8d5dc92f", @@ -92850,13 +108122,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92868,15 +108140,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "64af2cd469fee16a", @@ -92891,13 +108163,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-18", "versions": 1 @@ -92909,17 +108181,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1d8227ad3f3651a0", @@ -92934,15 +108206,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-18", "versions": 1 @@ -92954,17 +108226,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c0746df296544a3a", @@ -92979,15 +108251,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-18", "versions": 1 @@ -92999,17 +108271,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a2046dd883227b49", @@ -93024,15 +108296,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-18", "versions": 1 @@ -93044,17 +108316,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e9927c058ec0661f", @@ -93069,15 +108341,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-18", "versions": 1 @@ -93104,8 +108376,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-18", "versions": 1 @@ -93132,8 +108404,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-18", "versions": 1 @@ -93166,9 +108438,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Peak calling", "Read mapping", "Enrichment analysis", - "Peak calling", "Gene regulatory network analysis" ], "edam_topic": [], @@ -93182,9 +108454,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_rmdup", - "bowtie2", "bedtools_bamtofastq", + "bowtie2", + "samtools_rmdup", "macs2_callpeak" ], "update_time": "2024-07-12", @@ -93197,15 +108469,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "570172fbcf865e1d", @@ -93220,13 +108492,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93238,15 +108510,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "02e29499b946f3bb", @@ -93261,13 +108533,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93279,15 +108551,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "de24e5678f541584", @@ -93302,13 +108574,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93320,19 +108592,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "dbc650d226e89013", @@ -93347,27 +108619,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93379,19 +108651,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "7fb4dae5daab0522", @@ -93406,27 +108678,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93438,19 +108710,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "bb25ac3ba4863424", @@ -93465,27 +108737,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93497,15 +108769,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9edc78f665579559", @@ -93520,13 +108792,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93538,15 +108810,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "dc006ebf798f1f2f", @@ -93561,13 +108833,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93579,15 +108851,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "091f788edad78956", @@ -93602,13 +108874,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-11", "versions": 1 @@ -93620,17 +108892,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c20a68563e80d401", @@ -93645,15 +108917,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-11", "versions": 1 @@ -93665,17 +108937,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ddf222b797082436", @@ -93690,15 +108962,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-11", "versions": 1 @@ -93710,17 +108982,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b0b6dfa166b0d873", @@ -93735,15 +109007,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-11", "versions": 1 @@ -93770,8 +109042,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-11", "versions": 1 @@ -93798,8 +109070,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-11", "versions": 1 @@ -93811,17 +109083,17 @@ ], "doi": "", "edam_operation": [ - "Sequence annotation", - "Ab-initio gene prediction", - "Genome visualisation", - "Sequence assembly validation", "Gene prediction", - "Scaffolding", + "Mapping", "Homology-based gene prediction", "Genome assembly", - "Mapping", + "Scaffolding", + "Transcriptome assembly", "Operation", - "Transcriptome assembly" + "Sequence assembly validation", + "Ab-initio gene prediction", + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "ec3cc032a90c44f1", @@ -93840,14 +109112,14 @@ "genome-annotation" ], "tools": [ - "filter_by_fasta_ids", "gffread", - "export_remote", "fasta-stats", - "busco", - "jbrowse", + "export_remote", "bedtools_intersectbed", - "augustus" + "filter_by_fasta_ids", + "busco", + "augustus", + "jbrowse" ], "update_time": "2024-07-10", "versions": 19 @@ -93857,8 +109129,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "e790587f0a61fbad", @@ -93871,8 +109143,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deseq2", - "deg_annotate" + "deg_annotate", + "deseq2" ], "update_time": "2024-07-09", "versions": 5 @@ -93901,14 +109173,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-07-08", "versions": 0 @@ -93920,15 +109192,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "5199f404ad7ecef8", @@ -93943,13 +109215,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -93961,15 +109233,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "87d7a69106ca663d", @@ -93984,13 +109256,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94002,15 +109274,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c57f70d686b6062e", @@ -94025,13 +109297,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94043,19 +109315,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "885f0e66fa6b8790", @@ -94070,27 +109342,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94102,19 +109374,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "97c20a819394e381", @@ -94129,27 +109401,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94161,19 +109433,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "af5d714396856e9a", @@ -94188,27 +109460,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94220,15 +109492,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "75324d68ed124ff5", @@ -94243,13 +109515,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94261,15 +109533,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1f00e44f590b8369", @@ -94284,13 +109556,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94302,15 +109574,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4ca8b023f9a33440", @@ -94325,13 +109597,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-07-04", "versions": 1 @@ -94343,17 +109615,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ee27581327d147da", @@ -94368,15 +109640,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-04", "versions": 1 @@ -94388,17 +109660,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "cd4d88429f096fbc", @@ -94413,15 +109685,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-04", "versions": 1 @@ -94433,17 +109705,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e5f79f576548f7c5", @@ -94458,15 +109730,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-07-04", "versions": 1 @@ -94493,8 +109765,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-04", "versions": 1 @@ -94521,8 +109793,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-07-04", "versions": 1 @@ -94538,12 +109810,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "2d3063882d8239ff", @@ -94561,28 +109833,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-07-03", "versions": 1 @@ -94625,16 +109897,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", "Sequence contamination filtering", - "Statistical calculation", "Mapping", + "Statistical calculation", + "Sequencing quality control", "Sequence file editing", - "Validation" + "Formatting", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "cdea4f88ccbd155f", @@ -94651,18 +109923,18 @@ "qualityassessment" ], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "bedtools_genomecoveragebed", - "samtools_flagstat", - "picard_MarkDuplicates", "seqtk_sample", + "tasmanian_mismatch", "fastp", - "multiqc", "picard_CASM", - "tasmanian_mismatch", + "multiqc", "fastqc", + "bedtools_genomecoveragebed", + "picard_MarkDuplicates", "picard_CollectGcBiasMetrics", - "bowtie2" + "samtools_flagstat" ], "update_time": "2024-06-29", "versions": 1 @@ -94676,16 +109948,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", "Sequence contamination filtering", - "Statistical calculation", "Mapping", + "Statistical calculation", + "Sequencing quality control", "Sequence file editing", - "Validation" + "Formatting", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "1ddabc7d272dc702", @@ -94702,18 +109974,18 @@ "qualityassessment" ], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "bedtools_genomecoveragebed", - "samtools_flagstat", - "picard_MarkDuplicates", "seqtk_sample", + "tasmanian_mismatch", "fastp", - "multiqc", "picard_CASM", - "tasmanian_mismatch", + "multiqc", "fastqc", + "bedtools_genomecoveragebed", + "picard_MarkDuplicates", "picard_CollectGcBiasMetrics", - "bowtie2" + "samtools_flagstat" ], "update_time": "2024-06-28", "versions": 12 @@ -94724,12 +109996,12 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", + "Genome indexing", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "53fea86eb74c224b", @@ -94743,10 +110015,10 @@ "tags": [], "tools": [ "__FILTER_FAILED_DATASETS__", - "bwa", - "samtools_view", "fastp", - "multiqc" + "multiqc", + "bwa", + "samtools_view" ], "update_time": "2024-06-27", "versions": 4 @@ -94769,14 +110041,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2024-06-27", "versions": 1 @@ -94790,10 +110062,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "626260e3c3ee5c08", @@ -94808,20 +110080,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-06-27", "versions": 1 @@ -94835,10 +110107,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5361db01e3b6cc0c", @@ -94853,24 +110125,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -94884,10 +110156,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "375f5142c207a768", @@ -94902,24 +110174,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -94933,10 +110205,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7090bb14a7af15bd", @@ -94951,19 +110223,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -94977,10 +110249,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "cfa7c3d7e69e91d7", @@ -94995,19 +110267,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95021,10 +110293,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d2dec03b33af1b2f", @@ -95039,23 +110311,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95069,10 +110341,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e31abcc04c5c69bc", @@ -95087,23 +110359,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95117,10 +110389,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fff1a5c7475b3eeb", @@ -95135,19 +110407,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95161,10 +110433,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c66e2738f37a8c16", @@ -95179,19 +110451,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95205,10 +110477,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0b85fb10ed25d34e", @@ -95223,23 +110495,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95253,10 +110525,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9192807702bc3de2", @@ -95271,23 +110543,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-27", "versions": 1 @@ -95299,15 +110571,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ea5d2401f6711dff", @@ -95322,13 +110594,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95340,15 +110612,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "313d50268e1e22e4", @@ -95363,13 +110635,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95381,15 +110653,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "96cdba1fe599ada8", @@ -95404,13 +110676,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95422,19 +110694,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "cf3320614654adfe", @@ -95449,27 +110721,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95481,19 +110753,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "df24d76ebf13e3c1", @@ -95508,27 +110780,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95540,19 +110812,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "e58a87508a337b91", @@ -95567,27 +110839,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95599,15 +110871,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b3c8d64eca750ecf", @@ -95622,13 +110894,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95640,15 +110912,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2d6d74294e911fa3", @@ -95663,13 +110935,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95681,15 +110953,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "0d47009eb2d7bdc1", @@ -95704,13 +110976,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-27", "versions": 1 @@ -95722,17 +110994,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "150e288c2c2fe9e9", @@ -95747,15 +111019,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-27", "versions": 1 @@ -95767,17 +111039,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "58eeb06f911e8410", @@ -95792,15 +111064,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-27", "versions": 1 @@ -95812,17 +111084,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ace738014a7278b0", @@ -95837,15 +111109,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-27", "versions": 1 @@ -95872,8 +111144,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-27", "versions": 1 @@ -95900,8 +111172,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-27", "versions": 1 @@ -95911,17 +111183,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "d82db9c29b998f22", @@ -95934,13 +111206,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rna_star", "featurecounts", - "fasterq_dump", "multiqc", + "fasterq_dump", "collection_column_join", - "fastqc", "__FLATTEN__", + "fastqc", + "rna_star", "cutadapt" ], "update_time": "2024-06-26", @@ -95962,13 +111234,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gmx_setup", "__EXTRACT_DATASET__", - "gmx_editconf", - "pulchra", - "qiskit_xyz2pdb", "interactive_tool_qiskit_jupyter_notebook", "gmx_em", - "gmx_setup" + "qiskit_xyz2pdb", + "gmx_editconf", + "pulchra" ], "update_time": "2024-06-26", "versions": 2 @@ -95978,17 +111250,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Nucleic acid sequence analysis", - "Validation" + "Sequence trimming", + "Validation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d2f7fd589a91124a", @@ -96001,13 +111273,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "rna_star", "htseq_count", + "trimmomatic", "multiqc", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "deseq2" ], "update_time": "2024-06-25", "versions": 6 @@ -96021,9 +111293,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "8f5904693b5f74f4", @@ -96041,8 +111313,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-06-25", @@ -96057,15 +111329,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "cce88bc57b180d09", @@ -96083,18 +111355,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-06-25", "versions": 1 @@ -96127,24 +111399,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-06-25", "versions": 1 @@ -96158,19 +111430,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "574e42683dc3961b", @@ -96189,23 +111461,23 @@ "name:iwc" ], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-06-25", "versions": 1 @@ -96215,18 +111487,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "1f4dc0488f0554c6", @@ -96239,16 +111511,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", "freebayes", + "samtools_idxstats", + "trimmomatic", "multiqc", + "vcffilter2", + "bwa_mem", "fastqc", "bamFilter", - "samtools_idxstats" + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2024-06-20", "versions": 12 @@ -96262,10 +111534,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f794b4b9bb990c80", @@ -96280,20 +111552,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-06-20", "versions": 1 @@ -96307,10 +111579,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "918863756ce93725", @@ -96325,24 +111597,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96356,10 +111628,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e53b695ff681b675", @@ -96374,24 +111646,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96405,10 +111677,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6960b8f6c98a9b9e", @@ -96423,19 +111695,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96449,10 +111721,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "958b64b05011d8c0", @@ -96467,19 +111739,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96493,10 +111765,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ab490af27c9ccc80", @@ -96508,26 +111780,26 @@ "projects": [], "source": "https://usegalaxy.org", "tags": [ - "atac-seq" - ], - "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "atac-seq" + ], + "tools": [ + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96541,10 +111813,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "91ed290805f590de", @@ -96559,23 +111831,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96589,10 +111861,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "28b2550248a54d74", @@ -96607,19 +111879,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96633,10 +111905,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "25b8b5af30042d76", @@ -96651,19 +111923,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96677,10 +111949,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2b6245843e632c05", @@ -96695,23 +111967,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96725,10 +111997,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "019be65613876562", @@ -96743,23 +112015,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-20", "versions": 1 @@ -96771,15 +112043,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "162fda90525220de", @@ -96794,13 +112066,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -96812,15 +112084,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "875ff758068e1c2f", @@ -96835,13 +112107,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -96853,15 +112125,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "442949862ba62462", @@ -96876,13 +112148,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -96894,19 +112166,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "9e9a027e0c294a79", @@ -96921,27 +112193,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -96953,19 +112225,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "17f3d7e52777d2e8", @@ -96980,27 +112252,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -97012,19 +112284,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "a4a56efb37d845bf", @@ -97039,27 +112311,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -97071,15 +112343,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9990b6e2facf6dca", @@ -97094,13 +112366,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -97112,15 +112384,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "899f4f371b4c958c", @@ -97135,13 +112407,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -97153,15 +112425,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1829c91a30138721", @@ -97176,13 +112448,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-20", "versions": 1 @@ -97194,17 +112466,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7757cd56fa4d060c", @@ -97219,15 +112491,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-20", "versions": 1 @@ -97239,17 +112511,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c1339c998a55431c", @@ -97264,15 +112536,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-20", "versions": 1 @@ -97284,17 +112556,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "3d0ba2f11f370e05", @@ -97309,15 +112581,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-20", "versions": 1 @@ -97344,8 +112616,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-20", "versions": 1 @@ -97372,8 +112644,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-20", "versions": 1 @@ -97394,11 +112666,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "sort1", "Add_a_column1", + "Filter1", "Count1", - "Cut1", - "sort1", - "Filter1" + "Cut1" ], "update_time": "2024-06-14", "versions": 17 @@ -97419,11 +112691,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "sort1", "Add_a_column1", + "Filter1", "Count1", - "Cut1", - "sort1", - "Filter1" + "Cut1" ], "update_time": "2024-06-14", "versions": 11 @@ -97437,10 +112709,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c478d8de43a3f30f", @@ -97455,20 +112727,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-06-13", "versions": 1 @@ -97482,10 +112754,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a3ff7dbfadbd96e2", @@ -97500,24 +112772,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97531,10 +112803,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c07476a937b4e52e", @@ -97549,24 +112821,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97580,10 +112852,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f8d85cda81baa77d", @@ -97598,19 +112870,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97624,10 +112896,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "769ec5a187095b38", @@ -97642,19 +112914,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97668,10 +112940,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "357225c624e796b5", @@ -97686,23 +112958,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97716,10 +112988,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8db9ccf14567d9ba", @@ -97734,23 +113006,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97764,10 +113036,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b93a475af82a3d36", @@ -97782,19 +113054,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97808,10 +113080,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8ae311282a0d27a1", @@ -97826,19 +113098,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97852,10 +113124,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8a15bda6ce7a63ec", @@ -97870,23 +113142,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97900,10 +113172,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "226b506d1fc30e96", @@ -97918,23 +113190,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-13", "versions": 1 @@ -97946,15 +113218,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b893662378ed3da0", @@ -97969,13 +113241,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -97987,15 +113259,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "77d1505c0dd65e26", @@ -98010,13 +113282,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98028,15 +113300,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f9cd2289c007f103", @@ -98051,13 +113323,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98069,19 +113341,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "dff3cf6921b3d4d6", @@ -98096,27 +113368,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98128,19 +113400,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "59007e2bc9c807ee", @@ -98155,27 +113427,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98187,19 +113459,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "46e718fb8eeb4d54", @@ -98214,27 +113486,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98246,15 +113518,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "f733ad0a6cc50cb9", @@ -98269,13 +113541,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98287,15 +113559,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3823773ef4ecaaf4", @@ -98310,13 +113582,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98328,15 +113600,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1010a9b57c77239c", @@ -98351,13 +113623,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-13", "versions": 1 @@ -98369,17 +113641,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "607d1683d6e26cef", @@ -98394,15 +113666,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-13", "versions": 1 @@ -98414,17 +113686,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f3b417763495221b", @@ -98439,15 +113711,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-13", "versions": 1 @@ -98459,17 +113731,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1dd63a7b4c6f4c83", @@ -98484,15 +113756,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-13", "versions": 1 @@ -98519,8 +113791,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-13", "versions": 1 @@ -98547,8 +113819,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-13", "versions": 1 @@ -98559,8 +113831,8 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequencing quality control", "Formatting" ], @@ -98576,11 +113848,11 @@ "tags": [], "tools": [ "picard_NormalizeFasta", - "rbc_mirdeep2_mapper", "rbc_mirdeep2", "fastp", - "fastqc", - "rbc_mirdeep2_quantifier" + "rbc_mirdeep2_quantifier", + "rbc_mirdeep2_mapper", + "fastqc" ], "update_time": "2024-06-07", "versions": 7 @@ -98594,10 +113866,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f5200b7bcceed5d6", @@ -98612,20 +113884,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-06-06", "versions": 1 @@ -98639,10 +113911,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9b384b774485b2f2", @@ -98657,24 +113929,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98688,10 +113960,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "ef6036efe8a03a12", @@ -98706,19 +113978,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98732,10 +114004,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f8ed1ae9d501bb87", @@ -98750,19 +114022,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98776,10 +114048,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "19ce6cf93298e268", @@ -98794,23 +114066,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98824,10 +114096,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "63b0ce2faec558d5", @@ -98842,19 +114114,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98868,10 +114140,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c9474fcce2a21188", @@ -98886,19 +114158,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98912,10 +114184,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "85e2a1d6b1d4e3d7", @@ -98930,23 +114202,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-06-06", "versions": 1 @@ -98958,15 +114230,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ce815d36cbb57304", @@ -98981,13 +114253,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -98999,15 +114271,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "6e47a35cc5f2bdce", @@ -99022,13 +114294,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99040,15 +114312,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "47a2458ee9d57b24", @@ -99063,13 +114335,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99081,19 +114353,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "9eb29b71d7effefc", @@ -99108,27 +114380,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99140,19 +114412,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "cd824d8631d6a55e", @@ -99167,27 +114439,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99199,19 +114471,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "d00ac64dcd07f91a", @@ -99226,27 +114498,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99258,15 +114530,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "89f48993bb8f94bd", @@ -99281,13 +114553,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99299,15 +114571,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8756aabc654b1050", @@ -99322,13 +114594,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99340,15 +114612,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "75e23bc4e1ac2f5b", @@ -99363,13 +114635,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-06-06", "versions": 1 @@ -99381,17 +114653,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6ea1bd64873b6c18", @@ -99406,15 +114678,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-06", "versions": 1 @@ -99426,17 +114698,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "bcb798fb718968ce", @@ -99451,15 +114723,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-06", "versions": 1 @@ -99471,17 +114743,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "30ba39be60ec29be", @@ -99496,15 +114768,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-06-06", "versions": 1 @@ -99531,8 +114803,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-06-06", "versions": 1 @@ -99544,22 +114816,22 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Filtering", + "Gene prediction", + "Genome annotation", "Sequence clustering", - "Transcriptome assembly", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Differential gene expression analysis", - "Sequence assembly validation", - "Gene prediction", "Sequence motif recognition", + "Mapping assembly", "Scaffolding", - "Genome annotation", - "Genome assembly", + "Sequencing quality control", + "Cross-assembly", + "Transcriptome assembly", "Coding region prediction", - "Mapping assembly", - "Cross-assembly" + "De-novo assembly", + "Protein feature detection", + "Sequence assembly validation", + "Filtering" ], "edam_topic": [], "id": "c451e4dca9981ed0", @@ -99572,12 +114844,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "interproscan", + "prokka", "flye", - "filtlong", "antismash", "busco", - "prokka" + "interproscan", + "filtlong" ], "update_time": "2024-06-05", "versions": 4 @@ -99589,15 +114861,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "868acaf49d0743ec", @@ -99613,18 +114885,18 @@ "cloud-costs" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2024-06-04", "versions": 0 @@ -99661,14 +114933,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "e67b6da41e1e6932", @@ -99685,19 +114957,19 @@ "cloud-costs" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc", - "basil" + "basil", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-31", "versions": 5 @@ -99724,15 +114996,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-30", "versions": 1 @@ -99759,15 +115031,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-30", "versions": 1 @@ -99781,10 +115053,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "889b394b38b259eb", @@ -99799,20 +115071,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-05-30", "versions": 1 @@ -99826,10 +115098,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c75acc1ab44c121f", @@ -99844,24 +115116,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -99875,10 +115147,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "672ca09dce4b0dc3", @@ -99893,19 +115165,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -99919,10 +115191,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "05ef809e2b11154c", @@ -99937,19 +115209,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -99963,10 +115235,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "405dc14eb02ff234", @@ -99981,23 +115253,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -100011,10 +115283,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0dec1b9dbbb2f425", @@ -100029,19 +115301,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -100055,10 +115327,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "3fdd7a7907233d58", @@ -100073,19 +115345,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -100099,10 +115371,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2b820beaeb49dd64", @@ -100117,23 +115389,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-30", "versions": 1 @@ -100145,15 +115417,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c96b12be162f744b", @@ -100168,13 +115440,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100186,15 +115458,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "76d5143860fac947", @@ -100209,13 +115481,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", - "wig_to_bigWig", - "multiqc", - "macs2_callpeak", "bowtie2", - "cutadapt" + "macs2_callpeak", + "wig_to_bigWig", + "samtool_filter2", + "cutadapt", + "multiqc", + "tp_grep_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100227,19 +115499,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "96ae2544e22d34c5", @@ -100254,27 +115526,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100286,19 +115558,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "52e2b69787ca7a17", @@ -100313,27 +115585,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100345,15 +115617,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2078abc4c99c3344", @@ -100368,13 +115640,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100386,15 +115658,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "a8a38b594183db2b", @@ -100409,13 +115681,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-30", "versions": 1 @@ -100427,17 +115699,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "68495cc8ec3d46df", @@ -100452,15 +115724,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-30", "versions": 1 @@ -100472,17 +115744,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "32c769241ffce3d1", @@ -100497,15 +115769,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-30", "versions": 1 @@ -100532,8 +115804,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-05-30", "versions": 1 @@ -100545,14 +115817,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "d817e98cef94bc96", @@ -100569,18 +115841,18 @@ "cloud-costs" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-28", "versions": 0 @@ -100607,15 +115879,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-23", "versions": 1 @@ -100642,15 +115914,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-23", "versions": 1 @@ -100664,10 +115936,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "36c885b0bc829da3", @@ -100682,20 +115954,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-05-23", "versions": 1 @@ -100709,10 +115981,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a124d41da896779c", @@ -100727,24 +115999,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100758,10 +116030,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "13d9db3715f32b37", @@ -100776,19 +116048,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100802,10 +116074,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "adca3f2ca63730fe", @@ -100820,19 +116092,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100846,10 +116118,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7e56bee496344ddc", @@ -100864,23 +116136,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100894,10 +116166,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "46894456a9bec601", @@ -100912,19 +116184,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100938,10 +116210,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "68be9cfc0c58cb44", @@ -100956,19 +116228,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -100982,10 +116254,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "eab7347464872b4c", @@ -101000,23 +116272,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-23", "versions": 1 @@ -101028,15 +116300,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e1aad86fdf9e6616", @@ -101051,13 +116323,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101069,15 +116341,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "5532e6f775adb0d7", @@ -101092,13 +116364,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101110,19 +116382,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "ee3b8d7ba29da11c", @@ -101137,27 +116409,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101169,19 +116441,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "75fffbce810acaf3", @@ -101196,27 +116468,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101228,15 +116500,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1a23d8c795846251", @@ -101251,13 +116523,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101269,15 +116541,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3aa1b79aa6cca06b", @@ -101292,13 +116564,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-23", "versions": 1 @@ -101310,17 +116582,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6fa88ca75caba8e4", @@ -101335,15 +116607,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-23", "versions": 1 @@ -101355,17 +116627,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "676fa9af68f6a763", @@ -101380,15 +116652,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-23", "versions": 1 @@ -101415,8 +116687,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-05-23", "versions": 1 @@ -101443,15 +116715,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-16", "versions": 1 @@ -101478,15 +116750,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-16", "versions": 1 @@ -101500,10 +116772,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1c5a7196a442dd02", @@ -101518,20 +116790,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-05-16", "versions": 1 @@ -101545,10 +116817,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7185085cbe953cd9", @@ -101563,24 +116835,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101594,10 +116866,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e9aaa56af9d230d6", @@ -101612,19 +116884,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101638,10 +116910,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "eae5ae951abe6761", @@ -101656,19 +116928,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101682,10 +116954,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4ba61941f31f0215", @@ -101700,23 +116972,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101730,10 +117002,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "7a23e64dfa6957ce", @@ -101748,19 +117020,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101774,10 +117046,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "87ebf1b5956a61b5", @@ -101792,19 +117064,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101818,10 +117090,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "16910402667eec78", @@ -101836,23 +117108,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-16", "versions": 1 @@ -101864,15 +117136,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "6ecfa8ce19ed86da", @@ -101887,13 +117159,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -101905,15 +117177,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fd75347cfea06651", @@ -101928,13 +117200,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -101946,19 +117218,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "6a174e7498434bd5", @@ -101973,27 +117245,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -102005,19 +117277,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "2cc5472ad7c039d1", @@ -102032,27 +117304,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", - "bamFilter", - "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", - "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", "multiqc", - "bowtie2", + "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", + "macs2_callpeak", + "cat1", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -102064,15 +117336,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1cad9a0b375ed3d1", @@ -102087,13 +117359,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -102105,15 +117377,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4cc70b699ea8bc63", @@ -102128,13 +117400,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-16", "versions": 1 @@ -102146,17 +117418,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a986e4991fc61c92", @@ -102171,15 +117443,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-16", "versions": 1 @@ -102191,17 +117463,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "08da44d18689dffc", @@ -102216,15 +117488,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-16", "versions": 1 @@ -102251,8 +117523,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-05-16", "versions": 1 @@ -102263,11 +117535,11 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", + "Statistical calculation", + "Genome assembly", "Sequencing quality control", "Sequence assembly validation", "Scaffolding", - "Statistical calculation", - "Genome assembly", "Transcriptome assembly" ], "edam_topic": [], @@ -102281,10 +117553,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "spades", + "trimmomatic", "busco", - "trimmomatic" + "fastqc" ], "update_time": "2024-05-15", "versions": 1 @@ -102294,11 +117566,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequencing quality control", "Read mapping", - "Sequencing quality control" + "Data handling" ], "edam_topic": [], "id": "b1a98a2d5ebda1c5", @@ -102311,12 +117583,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "snpEff", - "rseqc_bam_stat", - "lofreq_call", "deepvariant", "fastqc", - "bowtie2" + "lofreq_call", + "rseqc_bam_stat" ], "update_time": "2024-05-14", "versions": 0 @@ -102343,15 +117615,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-09", "versions": 1 @@ -102365,10 +117637,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0775d8efad0dac10", @@ -102383,20 +117655,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-05-09", "versions": 1 @@ -102410,10 +117682,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b8ed069eea7879e7", @@ -102428,24 +117700,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102459,10 +117731,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "be46c5bb8c06a470", @@ -102477,19 +117749,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102503,10 +117775,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c5f4b7b2463f338b", @@ -102521,19 +117793,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102547,10 +117819,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e817b5b275b4952f", @@ -102565,23 +117837,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102595,10 +117867,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f7a3567ba6b57c9c", @@ -102613,19 +117885,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102639,10 +117911,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4f6e8ff94ca4f164", @@ -102657,19 +117929,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102683,10 +117955,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "deea71ccac30c7ea", @@ -102701,23 +117973,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-09", "versions": 1 @@ -102729,15 +118001,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fcae9dfcdca70798", @@ -102752,13 +118024,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -102770,15 +118042,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8e509c87d143022c", @@ -102793,13 +118065,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -102811,19 +118083,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "52bde903adbbaf60", @@ -102838,27 +118110,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -102870,19 +118142,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "eafe4aa62a600e1d", @@ -102897,27 +118169,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -102929,15 +118201,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7d11026214dd8c93", @@ -102952,13 +118224,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -102970,15 +118242,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "19c1ba21e82d8615", @@ -102993,13 +118265,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-09", "versions": 1 @@ -103011,17 +118283,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d768a4a06d3b1a90", @@ -103036,15 +118308,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-09", "versions": 1 @@ -103056,17 +118328,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2e029537d2f4ab50", @@ -103081,15 +118353,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-09", "versions": 1 @@ -103116,15 +118388,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-05-02", "versions": 1 @@ -103138,10 +118410,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a2b4a868fa9795d1", @@ -103156,20 +118428,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-05-02", "versions": 1 @@ -103183,10 +118455,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "870f4988a5cc815e", @@ -103201,24 +118473,24 @@ "atac-seq" ], "tools": [ - "table_compute", - "bedtools_bamtobed", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "bedtools_bamtobed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103232,10 +118504,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "9ecfaa613a112d78", @@ -103250,19 +118522,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103276,10 +118548,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1388fe5d8b50bc7c", @@ -103294,19 +118566,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103320,10 +118592,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "78249d353038002b", @@ -103338,23 +118610,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103368,10 +118640,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "962f784745c1b740", @@ -103386,19 +118658,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103412,10 +118684,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "4b92dfd20d48d479", @@ -103430,19 +118702,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103456,10 +118728,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "1f98df1adba71b98", @@ -103474,23 +118746,23 @@ "atac-seq" ], "tools": [ - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", - "samtools_view", - "param_value_from_file", - "tp_sorted_uniq", - "Filter1", + "macs2_callpeak", "wig_to_bigWig", + "Filter1", + "param_value_from_file", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "compose_text_param", - "tp_text_file_with_recurring_lines", - "split_file_to_collection", "multiqc", - "deeptools_bigwig_average", - "macs2_callpeak", + "table_compute", "bedtools_intersectbed", - "bedtools_multiintersectbed" + "split_file_to_collection", + "bedtools_multiintersectbed", + "tp_text_file_with_recurring_lines", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-05-02", "versions": 1 @@ -103502,15 +118774,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "de208a900880dcdc", @@ -103525,13 +118797,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103543,15 +118815,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ea61cd21e3fbad2b", @@ -103566,13 +118838,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103584,19 +118856,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "e0ec503626fa0d58", @@ -103611,27 +118883,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103643,19 +118915,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "85bc37a59a6ea443", @@ -103670,27 +118942,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103702,15 +118974,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "c707871e1dc9e21d", @@ -103725,13 +118997,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103743,15 +119015,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "716dc497d7d2e1c3", @@ -103766,13 +119038,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-05-02", "versions": 1 @@ -103784,17 +119056,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "291829fed6fa7c44", @@ -103809,15 +119081,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-02", "versions": 1 @@ -103829,17 +119101,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "803aec95399f7073", @@ -103854,15 +119126,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-05-02", "versions": 1 @@ -103873,13 +119145,13 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "Sequencing quality control", - "Variant calling", "Statistical calculation", - "Primer removal", "Read pre-processing", "Sequence trimming", - "DNA barcoding" + "Variant calling", + "DNA barcoding", + "Sequencing quality control", + "Primer removal" ], "edam_topic": [], "id": "5df593510c7d944d", @@ -103892,19 +119164,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "dada2_plotQualityProfile", + "dada2_makeSequenceTable", "fastq_paired_end_joiner", + "dada2_assignTaxonomyAddspecies", "trimmomatic", - "dada2_makeSequenceTable", + "dada2_plotQualityProfile", + "dada2_dada", "dada2_removeBimeraDenovo", - "dada2_mergePairs", "dada2_filterAndTrim", - "dada2_learnErrors", - "dada2_dada", "__SORTLIST__", + "dada2_learnErrors", + "dada2_mergePairs", "fastqc", - "cutadapt", - "dada2_assignTaxonomyAddspecies" + "cutadapt" ], "update_time": "2024-04-27", "versions": 1 @@ -103931,15 +119203,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-04-25", "versions": 1 @@ -103953,10 +119225,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e500078649dd026c", @@ -103971,20 +119243,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2024-04-25", "versions": 1 @@ -103998,10 +119270,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8182055f5ef561f3", @@ -104016,19 +119288,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-25", "versions": 1 @@ -104042,10 +119314,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "79527e2b83fd5c64", @@ -104060,19 +119332,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-25", "versions": 1 @@ -104086,10 +119358,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5bd6d7af64192b86", @@ -104104,19 +119376,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-25", "versions": 1 @@ -104130,10 +119402,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fda29ba2b6c98f8b", @@ -104148,19 +119420,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2024-04-25", "versions": 1 @@ -104172,15 +119444,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9ded318097694dbc", @@ -104195,13 +119467,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-04-25", "versions": 1 @@ -104213,19 +119485,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "0ebb1f5b6c9c8ab9", @@ -104240,27 +119512,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2024-04-25", "versions": 1 @@ -104272,15 +119544,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "72d134a60c694b59", @@ -104295,13 +119567,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-04-25", "versions": 1 @@ -104313,17 +119585,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f062eda543541ba8", @@ -104338,15 +119610,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-04-25", "versions": 1 @@ -104356,16 +119628,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", + "Transcriptome assembly", + "Sequence composition calculation", "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "8700f593a3d642f5", @@ -104378,18 +119650,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", - "gffcompare", "CONVERTER_gff_to_interval_index_0", - "trimmomatic", + "Filter1", "featurecounts", + "trimmomatic", "stringtie_merge", + "CONVERTER_gff_to_fli_0", + "deeptools_bam_coverage", + "fastqc", + "gffcompare", "stringtie", - "Filter1", "hisat2", - "fastqc", - "deseq2", - "CONVERTER_gff_to_fli_0" + "deseq2" ], "update_time": "2024-04-22", "versions": 0 @@ -104399,14 +119671,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "5415e85a86898e41", @@ -104421,19 +119693,19 @@ "bmb554-use-this" ], "tools": [ - "bwa_mem", - "__FILTER_FAILED_DATASETS__", - "collapse_dataset", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "fasterq_dump", + "lofreq_alnqual", "snpEff", - "fastp", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", - "lofreq_alnqual", + "multiqc", + "fastp", + "fasterq_dump", + "__FILTER_FAILED_DATASETS__", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view" ], "update_time": "2024-04-22", "versions": 4 @@ -104445,11 +119717,11 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", + "Enrichment analysis", "Formatting", - "Validation" + "Mapping" ], "edam_topic": [], "id": "aa9def6ec8f13b3a", @@ -104464,10 +119736,10 @@ "bmmb582" ], "tools": [ - "multiqc", "macs2_callpeak", - "picard_MarkDuplicates", - "bedtools_multiintersectbed" + "bedtools_multiintersectbed", + "multiqc", + "picard_MarkDuplicates" ], "update_time": "2024-04-19", "versions": 0 @@ -104492,10 +119764,10 @@ "bmmb582" ], "tools": [ - "bedtools_genomecoveragebed", + "collapse_dataset", "Add_a_column1", - "addValue", - "collapse_dataset" + "bedtools_genomecoveragebed", + "addValue" ], "update_time": "2024-04-18", "versions": 3 @@ -104522,8 +119794,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-18", "versions": 1 @@ -104539,11 +119811,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "69712265fdb10ed5", @@ -104573,8 +119845,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "6f1da4e0830e6051", @@ -104587,8 +119859,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-04-11", "versions": 1 @@ -104601,8 +119873,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "ebdf324634e7243c", @@ -104641,9 +119913,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2024-04-11", "versions": 1 @@ -104672,8 +119944,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2024-04-11", @@ -104731,8 +120003,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-11", "versions": 1 @@ -104742,11 +120014,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Visualisation", - "Taxonomic classification", "Pairwise sequence alignment", - "Box-Whisker plot plotting" + "Visualisation", + "Scatter plot plotting", + "Box-Whisker plot plotting", + "Taxonomic classification" ], "edam_topic": [], "id": "c3ea8fa3bb202dc6", @@ -104759,15 +120031,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "datamash_reverse", "kraken2", - "Cut1", - "join1", - "nanoplot", + "mergeCols1", "tp_replace_in_line", - "minimap2", "taxonomy_krona_chart", - "mergeCols1", - "datamash_reverse" + "nanoplot", + "join1", + "minimap2", + "Cut1" ], "update_time": "2024-04-05", "versions": 2 @@ -104777,14 +120049,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "0e5a3899ae97076b", @@ -104797,12 +120069,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "__FILTER_FAILED_DATASETS__", - "samtools_view", - "fasterq_dump", "fastp", - "multiqc" + "fasterq_dump", + "multiqc", + "bwa_mem", + "samtools_view" ], "update_time": "2024-04-02", "versions": 1 @@ -104825,11 +120097,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Show beginning1", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "Show beginning1", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2024-03-31", "versions": 0 @@ -104841,13 +120113,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "c8d74054c1820087", @@ -104860,10 +120132,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-03-28", "versions": 1 @@ -104886,14 +120158,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "MSGFPlusAdapter", - "DecoyDatabase", "FeatureFinderMultiplex", - "MetaProSIP", "FalseDiscoveryRate", + "MetaProSIP", "PeptideIndexer", "__SORTLIST__", - "IDMapper" + "IDMapper", + "MSGFPlusAdapter", + "DecoyDatabase" ], "update_time": "2024-03-28", "versions": 1 @@ -104921,8 +120193,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-03-28", "versions": 1 @@ -104932,9 +120204,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Sequence contamination filtering", - "Validation" + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "eb3409cc73e392a8", @@ -104949,8 +120221,8 @@ "veryshortintro" ], "tools": [ - "multiqc", - "fastp" + "fastp", + "multiqc" ], "update_time": "2024-03-25", "versions": 1 @@ -104978,8 +120250,8 @@ ], "tools": [ "taxonomy_krona_chart", - "Kraken2Tax", - "kraken2" + "kraken2", + "Kraken2Tax" ], "update_time": "2024-03-18", "versions": 0 @@ -104989,10 +120261,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Validation", "Sequencing quality control", "Formatting", - "Validation" + "Data handling" ], "edam_topic": [], "id": "b11796364c22235e", @@ -105007,10 +120279,10 @@ "transcriptomics" ], "tools": [ - "samtools_idxstats", - "picard_MarkDuplicates", + "rseqc_infer_experiment", "multiqc", - "rseqc_infer_experiment" + "samtools_idxstats", + "picard_MarkDuplicates" ], "update_time": "2024-03-18", "versions": 0 @@ -105020,12 +120292,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree reconstruction", - "Phylogenetic tree analysis", "Multiple sequence alignment", + "Phylogenetic tree generation", "Sequence analysis", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation" + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "9c4038fa15af6995", @@ -105038,9 +120310,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "iqtree", + "rbc_mafft", "newick_display", - "rbc_mafft" + "iqtree" ], "update_time": "2024-03-15", "versions": 1 @@ -105090,17 +120362,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence trimming", + "Read mapping" ], "edam_topic": [], "id": "eb33df15225b8aa0", @@ -105114,13 +120386,13 @@ "tags": [], "tools": [ "gatk4_mutect2", - "bwa_mem", - "picard_MarkDuplicates", + "samtools_sort", "vcffilter2", + "picard_AddOrReplaceReadGroups", "trim_galore", - "samtools_sort", + "bwa_mem", "fastqc", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2024-03-14", "versions": 1 @@ -105133,8 +120405,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "ecf3a7f9da7409ef", @@ -105149,17 +120421,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-03-14", "versions": 1 @@ -105238,14 +120510,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-03-14", "versions": 1 @@ -105255,14 +120527,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", "Statistical calculation", + "Genome assembly", + "Sequencing quality control", "Sequence composition calculation", - "Taxonomic classification", + "Sequence alignment analysis", "Read mapping", - "Sequencing quality control", - "Genome assembly" + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "e0c33057ac2670ba", @@ -105275,14 +120547,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bg_diamond_makedb", + "bowtie2", "trimmomatic", - "kraken", + "spades", "fasterq_dump", "bg_diamond", "fastqc", - "spades", - "bowtie2" + "kraken", + "bg_diamond_makedb" ], "update_time": "2024-03-13", "versions": 11 @@ -105292,11 +120564,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -105311,8 +120583,8 @@ "tags": [], "tools": [ "fastqc", - "fastqe", - "cutadapt" + "cutadapt", + "fastqe" ], "update_time": "2024-03-08", "versions": 5 @@ -105326,9 +120598,9 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence file editing", "Nucleic acid sequence analysis", - "Sequence file editing" + "Data handling" ], "edam_topic": [], "id": "51f936d1a4e849fa", @@ -105343,17 +120615,17 @@ "nebnext" ], "tools": [ - "presto_parselog", + "presto_filterseq", + "seqtk_sample", + "presto_parseheaders", "presto_pairseq", + "prestor_abseq3", "presto_partition", - "seqtk_sample", "presto_assemblepairs", + "presto_parselog", "presto_buildconsensus", - "__UNZIP_COLLECTION__", "presto_collapseseq", - "presto_parseheaders", - "presto_filterseq", - "prestor_abseq3", + "__UNZIP_COLLECTION__", "presto_maskprimers" ], "update_time": "2024-03-08", @@ -105367,9 +120639,9 @@ ], "doi": "", "edam_operation": [ - "Data handling", + "Sequence file editing", "Nucleic acid sequence analysis", - "Sequence file editing" + "Data handling" ], "edam_topic": [], "id": "34f3aac3aed0f97a", @@ -105384,17 +120656,17 @@ "nebnext" ], "tools": [ - "presto_parselog", + "presto_filterseq", + "seqtk_sample", + "presto_parseheaders", "presto_pairseq", + "prestor_abseq3", "presto_partition", - "seqtk_sample", "presto_assemblepairs", + "presto_parselog", "presto_buildconsensus", - "__UNZIP_COLLECTION__", "presto_collapseseq", - "presto_parseheaders", - "presto_filterseq", - "prestor_abseq3", + "__UNZIP_COLLECTION__", "presto_maskprimers" ], "update_time": "2024-03-07", @@ -105411,11 +120683,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "be7dab2274c1acdd", @@ -105445,8 +120717,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "bff8bc8d0059274f", @@ -105461,11 +120733,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-03-07", "versions": 1 @@ -105478,8 +120750,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "fd511165e30cb62c", @@ -105492,8 +120764,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-03-07", "versions": 1 @@ -105506,8 +120778,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "92b67534076ae889", @@ -105549,17 +120821,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2024-03-07", "versions": 1 @@ -105569,9 +120841,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "334c4fe8929b5029", @@ -105594,17 +120866,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", + "Mapping", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Read pre-processing", - "Mapping", - "Sequence trimming" + "Sequence alignment analysis", + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "a89008fccc1f1d17", @@ -105617,14 +120889,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", "bowtie2", - "picard_MarkDuplicates", + "pe_histogram", + "deeptools_bam_coverage", "bedtools_bamtobed", "fastqc", "bamFilter", "cutadapt", - "pe_histogram" + "picard_MarkDuplicates" ], "update_time": "2024-02-22", "versions": 4 @@ -105640,11 +120912,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "8e6d24a14d2908c2", @@ -105674,16 +120946,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "49c9e8161a46667f", @@ -105699,16 +120971,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-02-22", "versions": 1 @@ -105720,13 +120992,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "0602c14704dbe1ff", @@ -105739,10 +121011,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-02-15", "versions": 1 @@ -105755,16 +121027,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "8ccb42012dcb5db2", @@ -105779,17 +121051,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-02-15", "versions": 1 @@ -105810,11 +121082,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "keras_model_config", - "ml_visualization_ex", "model_prediction", "keras_train_and_eval", - "keras_model_builder" + "keras_model_config", + "keras_model_builder", + "ml_visualization_ex" ], "update_time": "2024-02-08", "versions": 0 @@ -105837,11 +121109,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "keras_model_config", - "ml_visualization_ex", "model_prediction", "keras_train_and_eval", - "keras_model_builder" + "keras_model_config", + "keras_model_builder", + "ml_visualization_ex" ], "update_time": "2024-02-08", "versions": 0 @@ -105900,9 +121172,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-02-08", "versions": 1 @@ -105929,15 +121201,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2024-02-08", "versions": 1 @@ -105949,13 +121221,13 @@ ], "doi": "", "edam_operation": [ - "Aggregation", + "Sequence composition calculation", "Visualisation", "Statistical calculation", - "Sequence composition calculation", "Taxonomic classification", + "Validation", "Sequencing quality control", - "Validation" + "Aggregation" ], "edam_topic": [], "id": "7321c6ad5425d347", @@ -105969,12 +121241,12 @@ "tags": [], "tools": [ "kraken2", - "taxonomy_krona_chart", + "krakentools_kreport2krona", "multiqc", + "taxonomy_krona_chart", "kraken-report", - "interactive_tool_pavian", "fastqc", - "krakentools_kreport2krona" + "interactive_tool_pavian" ], "update_time": "2024-02-01", "versions": 1 @@ -106034,17 +121306,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Formatting", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "b26501a4a85bfdeb", @@ -106057,18 +121329,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpSift_extractFields", - "fastq_dump", - "snpEff", "samtools_stats", + "snpEff", + "snpSift_extractFields", + "lofreq_viterbi", "fastp", "multiqc", - "lofreq_viterbi", "lofreq_indelqual", + "bwa_mem", + "fastqc", "lofreq_call", - "fastqc" + "fastq_dump", + "picard_MarkDuplicates" ], "update_time": "2024-01-25", "versions": 5 @@ -106078,18 +121350,18 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence assembly validation", "Visualisation", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Validation" + "Sequence assembly validation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "7a33bc2d0970b502", @@ -106102,16 +121374,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "velveth", - "fastqe", - "quast", - "fastq_paired_end_interlacer", "cshl_fastq_quality_filter", - "velvetg", + "bowtie2", "samtools_stats", "multiqc", + "fastqe", + "velvetg", + "fastq_paired_end_interlacer", + "velveth", + "quast", "fastqc", - "bowtie2", "cutadapt" ], "update_time": "2024-01-25", @@ -106122,17 +121394,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Formatting", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "4de095b92ed661ac", @@ -106145,18 +121417,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpSift_extractFields", - "fastq_dump", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", + "fastp", "multiqc", - "fastqc" + "lofreq_indelqual", + "bwa_mem", + "fastqc", + "lofreq_call", + "fastq_dump", + "picard_MarkDuplicates" ], "update_time": "2024-01-25", "versions": 0 @@ -106166,19 +121438,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Visualisation", - "Read summarisation", "Statistical calculation", + "Visualisation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "582f3de3971fc38c", @@ -106191,17 +121463,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "tp_sort_header_tool", - "rna_star", "featurecounts", + "multiqc", "fasterq_dump", - "pygenomeTracks", - "rseqc_infer_experiment", "gtftobed12", - "multiqc", + "tp_sort_header_tool", "__FLATTEN__", - "cutadapt" + "fastqc", + "rna_star", + "cutadapt", + "rseqc_infer_experiment", + "pygenomeTracks" ], "update_time": "2024-01-25", "versions": 0 @@ -106211,19 +121483,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Visualisation", - "Read summarisation", "Statistical calculation", + "Visualisation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "e33f6a058c5f57e5", @@ -106236,17 +121508,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "tp_sort_header_tool", - "rna_star", - "fastq_dump", - "pygenomeTracks", - "rseqc_infer_experiment", "featurecounts", - "gtftobed12", "multiqc", + "gtftobed12", + "tp_sort_header_tool", + "rseqc_infer_experiment", "__FLATTEN__", - "cutadapt" + "fastqc", + "rna_star", + "cutadapt", + "fastq_dump", + "pygenomeTracks" ], "update_time": "2024-01-25", "versions": 0 @@ -106256,18 +121528,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Generation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Sequence trimming", - "Genome visualisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Generation", "Genome indexing", + "Sequence composition calculation", + "Sequence trimming", + "Read mapping", + "Genome visualisation", "SNP detection" ], "edam_topic": [], @@ -106281,17 +121553,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "snpSift_extractFields", "samtools_stats", + "snpSift_extractFields", + "cutadapt", "lofreq_viterbi", - "lofreq_call", - "jbrowse", + "snpeff_sars_cov_2", "lofreq_indelqual", + "bwa_mem", "fastqc", - "cutadapt" + "lofreq_call", + "jbrowse", + "picard_MarkDuplicates" ], "update_time": "2024-01-24", "versions": 1 @@ -106301,17 +121573,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Sequence trimming", - "Genome visualisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence trimming", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "5b2bb861501fa248", @@ -106324,10 +121596,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "bwa_mem", + "jbrowse", "cutadapt", - "jbrowse" + "bwa_mem", + "fastqc" ], "update_time": "2024-01-24", "versions": 1 @@ -106337,12 +121609,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "RNA-Seq quantification" + "Read mapping" ], "edam_topic": [], "id": "efa598aa9b7cb0b1", @@ -106355,10 +121627,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "qualimap_bamqc", "bowtie2", - "featurecounts" + "featurecounts", + "fastqc" ], "update_time": "2024-01-23", "versions": 1 @@ -106368,15 +121640,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Validation" + "Validation", + "Read mapping" ], "edam_topic": [], "id": "e7586d70715207b5", @@ -106390,14 +121662,14 @@ "tags": [], "tools": [ "bowtie2", - "picard_MarkDuplicates", "snpEff", + "vcftools_annotate", "deepvariant", "multiqc", - "fastqc", "__FLATTEN__", - "vcftools_annotate", - "cutadapt" + "fastqc", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-01-22", "versions": 38 @@ -106410,18 +121682,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "d3f35215e6f45d79", @@ -106437,19 +121709,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-01-18", "versions": 1 @@ -106462,19 +121734,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "31a6145b0832fa48", @@ -106490,20 +121762,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-01-18", "versions": 1 @@ -106515,18 +121787,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "8b81b9a3b49bbf98", @@ -106543,21 +121815,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2024-01-18", "versions": 1 @@ -106570,11 +121842,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "786aa9e2bd723629", @@ -106590,15 +121862,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-01-18", "versions": 1 @@ -106608,12 +121880,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "ba347b695dbff2ea", @@ -106626,14 +121898,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "samtools_view", + "bowtie2", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "bcftools_norm", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 1 @@ -106643,14 +121915,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "ff35347c4e2f0e81", @@ -106663,11 +121935,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_view", "samtools_rmdup", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106677,12 +121949,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "496b0e8a0e5a4191", @@ -106695,13 +121967,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106733,11 +122005,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "cd4b5b62f1eed51b", @@ -106750,11 +122022,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106762,17 +122034,17 @@ { "create_time": "2024-01-13", "creators": [], - "doi": "", - "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", + "doi": "", + "edam_operation": [ "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "c75fcf2b7ba057fd", @@ -106785,15 +122057,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "bwa_mem", - "gemini_load", - "samtools_view", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "bcftools_norm", + "gemini_load", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106803,11 +122075,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "d5062ef48aa246d8", @@ -106820,11 +122092,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106834,11 +122106,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "76fff93650152579", @@ -106851,9 +122123,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "bowtie2", - "multiqc" + "multiqc", + "fastqc" ], "update_time": "2024-01-13", "versions": 0 @@ -106863,15 +122135,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "371b242d97f2f030", @@ -106884,14 +122156,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "bwa_mem", - "samtools_view", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "bcftools_norm", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106901,12 +122173,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "70dacee3da375e2b", @@ -106919,13 +122191,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "snpEff", - "freebayes", + "bowtie2", "samtools_stats", - "vcfallelicprimitives", + "freebayes", + "snpEff", "multiqc", - "fastqc", - "bowtie2" + "vcfallelicprimitives", + "fastqc" ], "update_time": "2024-01-13", "versions": 0 @@ -106935,11 +122207,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "f2d3abc6c45c4839", @@ -106952,11 +122224,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106966,12 +122238,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "9bf1d223a57f88da", @@ -106984,12 +122256,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", "freebayes", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -106999,12 +122271,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "1b57987895f8ca9e", @@ -107017,13 +122289,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 1 @@ -107033,11 +122305,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "d3704f2927e3065e", @@ -107050,10 +122322,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "samtools_stats", "bowtie2", - "multiqc" + "samtools_stats", + "multiqc", + "fastqc" ], "update_time": "2024-01-13", "versions": 0 @@ -107063,15 +122335,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Genome visualisation", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence trimming", "Read pre-processing", - "Sequence trimming" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "49c61c378cacfe02", @@ -107084,11 +122356,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "freebayes", - "jbrowse", + "cutadapt", "fastqc", - "bowtie2", - "cutadapt" + "jbrowse" ], "update_time": "2024-01-13", "versions": 1 @@ -107098,15 +122370,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "e64a6119053cb126", @@ -107119,12 +122391,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_view", "samtools_rmdup", "freebayes", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "samtools_view" ], "update_time": "2024-01-13", "versions": 1 @@ -107134,12 +122406,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "08f58af7b6cc0ab6", @@ -107152,14 +122424,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "samtools_view", + "bowtie2", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "bcftools_norm", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 1 @@ -107169,11 +122441,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "0e6a842034ca9aec", @@ -107186,9 +122458,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "bowtie2", - "multiqc" + "multiqc", + "fastqc" ], "update_time": "2024-01-13", "versions": 0 @@ -107198,11 +122470,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping" ], "edam_topic": [], "id": "a0451d7084d7732b", @@ -107215,12 +122487,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", + "bowtie2", + "freebayes", "samtools_rmdup", "snpEff", - "freebayes", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -107230,12 +122502,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "48963532e030de6c", @@ -107248,14 +122520,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "samtools_view", + "bowtie2", "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "bcftools_norm", "multiqc", "fastqc", - "bowtie2" + "samtools_view" ], "update_time": "2024-01-13", "versions": 0 @@ -107276,13 +122548,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_sort_header_tool", - "get_flanks1", "CONVERTER_interval_to_bed_0", + "tp_tail_tool", + "tp_sort_header_tool", + "gops_intersect_1", "Grouping1", "tp_replace_in_column", - "gops_intersect_1", - "tp_tail_tool" + "get_flanks1" ], "update_time": "2024-01-13", "versions": 0 @@ -107303,13 +122575,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mimodd_varreport", + "snpEff", "snpEff_download", + "mimodd_varreport", "mimodd_varextract", + "mimodd_varcall", "mimodd_vcf_filter", - "snpEff", - "mimodd_map", - "mimodd_varcall" + "mimodd_map" ], "update_time": "2024-01-13", "versions": 0 @@ -107319,16 +122591,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b6d90898e2db6aba", @@ -107342,20 +122614,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "tp_sort_header_tool", + "samtools_idxstats", + "snpEff", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107365,16 +122637,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2497103d279cd20e", @@ -107387,21 +122659,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", + "snpEff", + "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107411,13 +122683,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", + "Read mapping", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "0d8ec47a84766f96", @@ -107430,21 +122702,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107454,13 +122726,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation", "Sequence composition calculation", - "Mapping", + "Statistical calculation", + "Sequence alignment", + "Variant calling", "Sequencing quality control", "Formatting", - "Sequence alignment" + "Mapping" ], "edam_topic": [], "id": "5951d11d3122abed", @@ -107473,20 +122745,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bwa_mem2", "picard_CollectInsertSizeMetrics", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "tp_sort_header_tool", + "samtools_idxstats", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "bwa_mem2", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2024-01-10", "versions": 3 @@ -107496,16 +122768,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ba68fd4b4348e63c", @@ -107518,20 +122790,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "Filter1", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "picard_CollectInsertSizeMetrics", + "freebayes", "vcffilter2", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107541,16 +122813,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2af3de32c630e1b4", @@ -107563,21 +122835,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_coveragebed", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "snpEff", "vcffilter2", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "snpSift_filter" + "snpSift_filter", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107587,16 +122859,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e2c77aeabb8053b4", @@ -107609,22 +122881,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bowtie2", + "Filter1", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "picard_CollectInsertSizeMetrics", + "freebayes", "vcffilter2", - "Summary_Statistics1", "vcfvcfintersect", - "freebayes", - "samtool_filter2", + "tp_sort_header_tool", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107634,16 +122906,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e67db5dc8eab60f3", @@ -107656,20 +122928,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", + "snpEff", + "vcffilter2", + "bam_to_sam", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107679,16 +122951,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f23e5f333987a89f", @@ -107702,19 +122974,19 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "tp_sort_header_tool", + "samtools_idxstats", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 5 @@ -107724,16 +122996,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "449a419bcfd3c49e", @@ -107746,23 +123018,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "bedtools_coveragebed", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "samtools_idxstats", + "snpEff", + "snpSift_extractFields", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpSift_extractFields", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107772,16 +123044,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "a89eaad3f42ec41c", @@ -107794,21 +123066,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "bedtools_coveragebed", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "samtools_idxstats", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107818,16 +123090,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4e3efbdd0c4c3e64", @@ -107840,21 +123112,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "bedtools_coveragebed", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "samtools_idxstats", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-10", "versions": 0 @@ -107864,16 +123136,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "c9e442a395fc1a58", @@ -107886,20 +123158,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", + "vcffilter2", + "bam_to_sam", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -107909,16 +123181,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "01585f1230125ba1", @@ -107931,19 +123203,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", + "vcffilter2", + "bam_to_sam", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -107953,16 +123225,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d7e14ff032a6ac4f", @@ -107975,21 +123247,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bowtie2", + "Filter1", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "picard_CollectInsertSizeMetrics", + "freebayes", "vcffilter2", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -107999,16 +123271,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "67e3457099db3ed2", @@ -108021,19 +123293,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_coveragebed", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", "vcffilter2", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -108043,16 +123315,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b50f2446d5e60334", @@ -108065,22 +123337,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", + "snpEff", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -108090,16 +123362,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5eb2e090df59d9a9", @@ -108112,22 +123384,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 1 @@ -108137,16 +123409,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b16a1642e2cd54a2", @@ -108159,21 +123431,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -108183,16 +123455,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8689dc9eac10c871", @@ -108205,20 +123477,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "Filter1", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "picard_CollectInsertSizeMetrics", + "freebayes", "vcffilter2", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 0 @@ -108228,16 +123500,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "bfd3ba54576d2d81", @@ -108250,22 +123522,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", + "snpEff", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 1 @@ -108275,13 +123547,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", + "Read mapping", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "c11dfc3314e33b33", @@ -108294,18 +123566,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", "freebayes", - "samtool_filter2", + "vcffilter2", + "bam_to_sam", "fastqc", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-09", "versions": 2 @@ -108315,16 +123587,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "dbdc894ad54675a8", @@ -108337,21 +123609,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-08", "versions": 1 @@ -108361,16 +123633,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b9e6ddbc79904844", @@ -108384,18 +123656,18 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "snpEff", "freebayes", - "samtool_filter2", + "snpEff", + "vcffilter2", + "bam_to_sam", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-08", "versions": 1 @@ -108405,16 +123677,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "edb299ecbf147618", @@ -108428,17 +123700,17 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", "freebayes", - "samtool_filter2", + "vcffilter2", + "bam_to_sam", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2024-01-08", "versions": 0 @@ -108454,11 +123726,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "b73e416c06790ac5", @@ -108506,9 +123778,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2023-12-28", "versions": 1 @@ -108529,14 +123801,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "fastq_to_fasta_python", + "tab2fasta", "fastq_join", - "fastq_groomer", "fasta2tab", - "fasta_filter_by_length", "Grep1", - "tab2fasta", + "fasta_filter_by_length", "cshl_fastx_collapser", - "fastq_to_fasta_python" + "fastq_groomer" ], "update_time": "2023-12-17", "versions": 4 @@ -108548,23 +123820,23 @@ ], "doi": "", "edam_operation": [ - "Coding region prediction", - "De-novo assembly", + "Genome annotation", + "Sequence contamination filtering", + "Scaffolding", "Phylogenetic tree analysis", "Sequencing quality control", - "Genome assembly", - "Variant calling", - "Phylogenetic tree generation", - "Phasing", + "Coding region prediction", "k-mer counting", + "Sequence analysis", "Gene prediction", - "Genome annotation", - "Sequence contamination filtering", - "Scaffolding", - "Taxonomic classification", + "Phylogenetic tree generation", + "Genome assembly", + "Phasing", + "De-novo assembly", + "Variant calling", + "Validation", "Phylogenetic tree visualisation", - "Sequence analysis", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "d4f0a7ccb09f1e55", @@ -108582,18 +123854,18 @@ "workflow" ], "tools": [ - "snippy_core", "Kraken2Tax", - "kraken2", - "snippy", + "prokka", "raxml", - "snp_dists", + "kraken2", + "merqury", "fastp", - "shovill", - "prokka", "multiqc", + "snippy_core", + "snippy", + "snp_dists", "staramr_search", - "merqury" + "shovill" ], "update_time": "2023-12-13", "versions": 10 @@ -108603,12 +123875,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence composition calculation", "Visualisation", "Statistical calculation", - "Sequence composition calculation", - "Taxonomic classification", - "Sequencing quality control" + "Sequencing quality control", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "5b74b780d3955eb3", @@ -108621,10 +123893,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "taxonomy_krona_chart", "fastq_dump", - "kraken2" + "taxonomy_krona_chart", + "kraken2", + "fastqc" ], "update_time": "2023-12-08", "versions": 0 @@ -108637,8 +123909,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "1a08efa0bf83d225", @@ -108651,8 +123923,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2023-12-07", "versions": 1 @@ -108665,8 +123937,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "ff84d87fd3638a3f", @@ -108694,10 +123966,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "3d7a9694bcee6db5", @@ -108712,20 +123984,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-12-07", "versions": 1 @@ -108739,10 +124011,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d6cf3be79a4b7db4", @@ -108757,19 +124029,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-12-07", "versions": 1 @@ -108783,10 +124055,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "68b995393b3142ec", @@ -108801,19 +124073,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-12-07", "versions": 1 @@ -108823,8 +124095,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "030814e5329ea62d", @@ -108837,9 +124109,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "__TAG_FROM_FILE__", "deseq2", - "__BUILD_LIST__", - "__TAG_FROM_FILE__" + "__BUILD_LIST__" ], "update_time": "2023-12-07", "versions": 24 @@ -108849,12 +124121,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Sequence assembly validation", "Genome annotation", + "Genome assembly", + "Sequence assembly validation", "Scaffolding", + "Genome visualisation", "Sequence annotation", - "Genome assembly", "Transcriptome assembly" ], "edam_topic": [], @@ -108868,12 +124140,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "maker_map_ids", "jcvi_gff_stats", "gffread", - "maker", "fasta-stats", "busco", + "maker_map_ids", + "maker", "jbrowse" ], "update_time": "2023-12-04", @@ -108900,18 +124172,18 @@ "generic" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -108940,14 +124212,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-30", "versions": 1 @@ -108961,20 +124233,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3db4eb1ecb588d44", @@ -108990,22 +124262,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -109018,18 +124290,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "4a0ad87aa5aa558a", @@ -109045,19 +124317,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -109084,8 +124356,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-30", "versions": 1 @@ -109112,8 +124384,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-30", "versions": 1 @@ -109126,16 +124398,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "eaf96fa3c39c210b", @@ -109151,16 +124423,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -109173,13 +124445,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -109195,19 +124467,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-30", "versions": 1 @@ -109234,15 +124506,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-11-30", "versions": 1 @@ -109255,19 +124527,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "2b41752b8518a87b", @@ -109283,20 +124555,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -109310,10 +124582,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5aa4b9131c31cb79", @@ -109328,20 +124600,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-11-30", "versions": 1 @@ -109355,10 +124627,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "8cf06b14037a8d5a", @@ -109373,19 +124645,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-30", "versions": 1 @@ -109399,10 +124671,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "438761debd08a9be", @@ -109417,19 +124689,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-30", "versions": 1 @@ -109441,17 +124713,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "326ced2230a49c26", @@ -109466,15 +124738,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -109486,14 +124758,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "34ab5572a9547bfe", @@ -109509,18 +124781,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -109543,15 +124815,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2023-11-30", "versions": 1 @@ -109574,21 +124846,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -109611,21 +124883,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -109648,19 +124920,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2023-11-30", "versions": 1 @@ -109688,8 +124960,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-30", "versions": 1 @@ -109717,17 +124989,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2023-11-30", "versions": 1 @@ -109753,20 +125025,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -109778,15 +125050,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "15a0e22570f71098", @@ -109804,17 +125076,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -109824,16 +125096,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4f459cfef6108e75", @@ -109846,21 +125118,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-11-28", "versions": 0 @@ -109889,8 +125161,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "cff93a6f24af5fee", @@ -109903,8 +125175,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deseq2", - "__TAG_FROM_FILE__" + "__TAG_FROM_FILE__", + "deseq2" ], "update_time": "2023-11-24", "versions": 1 @@ -109914,8 +125186,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "c8ee2da45b6889b9", @@ -109928,8 +125200,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deseq2", - "__TAG_FROM_FILE__" + "__TAG_FROM_FILE__", + "deseq2" ], "update_time": "2023-11-24", "versions": 0 @@ -109939,13 +125211,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", + "Transcriptome assembly", + "Sequence alignment", "Differential gene expression analysis", "Sequencing quality control", - "Sequence alignment", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "27144c7e44d3f56b", @@ -109959,11 +125231,11 @@ "tags": [], "tools": [ "trimmomatic", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "stringtie" + "stringtie", + "hisat2", + "deseq2" ], "update_time": "2023-11-23", "versions": 1 @@ -109992,14 +125264,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-23", "versions": 1 @@ -110013,20 +125285,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "7f6900852a81d121", @@ -110042,22 +125314,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-23", "versions": 1 @@ -110084,8 +125356,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-23", "versions": 1 @@ -110098,16 +125370,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "3753dcca4100e976", @@ -110123,16 +125395,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-23", "versions": 1 @@ -110145,16 +125417,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "c09b8a0c96123cbb", @@ -110170,16 +125442,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-23", "versions": 1 @@ -110192,13 +125464,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -110214,19 +125486,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-23", "versions": 1 @@ -110239,13 +125511,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -110261,19 +125533,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-23", "versions": 1 @@ -110300,15 +125572,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-11-23", "versions": 1 @@ -110335,15 +125607,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", "tp_find_and_replace", - "fasterq_dump", - "cat_multi_datasets", "compose_text_param", "__APPLY_RULES__", - "__RELABEL_FROM_FILE__", + "fasterq_dump", + "split_file_to_collection", "map_param_value", - "split_file_to_collection" + "cat_multi_datasets", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2023-11-23", "versions": 1 @@ -110371,8 +125643,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-23", "versions": 1 @@ -110400,8 +125672,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-23", "versions": 1 @@ -110411,11 +125683,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Data handling" ], "edam_topic": [], "id": "5cb86cdc33296cc2", @@ -110428,12 +125700,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "fastq_dump", + "cufflinks", "samtools_sort", + "fastqc", "hisat2", - "cufflinks", - "fastqc" + "fastq_dump", + "cuffdiff" ], "update_time": "2023-11-20", "versions": 0 @@ -110443,8 +125715,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "8a350e0d96e937a5", @@ -110457,8 +125729,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "spades", "bandage_image", + "spades", "bandage_info" ], "update_time": "2023-11-19", @@ -110488,14 +125760,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-16", "versions": 1 @@ -110508,8 +125780,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "85f521f5c7351406", @@ -110524,11 +125796,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-16", "versions": 1 @@ -110542,10 +125814,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b7b69aaee5202144", @@ -110560,20 +125832,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-11-16", "versions": 1 @@ -110587,10 +125859,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "f58aa85ceaa19534", @@ -110605,19 +125877,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-16", "versions": 1 @@ -110631,10 +125903,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5b540de61a70df64", @@ -110649,19 +125921,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-11-16", "versions": 1 @@ -110671,14 +125943,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "eb01b539d17580c3", @@ -110700,10 +125972,10 @@ "multiple" ], "tools": [ - "trimmomatic", "featurecounts", - "hisat2", + "trimmomatic", "fastqc", + "hisat2", "deseq2" ], "update_time": "2023-11-13", @@ -110731,8 +126003,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -110759,8 +126031,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -110783,19 +126055,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2023-11-13", "versions": 1 @@ -110805,9 +126077,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "bcce65725298ff33", @@ -110830,11 +126102,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -110848,8 +126120,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2023-11-12", "versions": 1 @@ -110859,13 +126131,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Visualisation", "Sequence contamination filtering", + "Sequence composition calculation", + "Visualisation", "Statistical calculation", "Taxonomic classification", - "Sequence composition calculation", - "Sequencing quality control" + "Sequencing quality control", + "Aggregation" ], "edam_topic": [], "id": "60f0d0d5d6e93941", @@ -110878,13 +126150,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "kraken2", - "porechop", - "taxonomy_krona_chart", + "krakentools_kreport2krona", "fastp", - "fastqc", - "Filter1", - "krakentools_kreport2krona" + "taxonomy_krona_chart", + "porechop", + "fastqc" ], "update_time": "2023-11-10", "versions": 0 @@ -110951,14 +126223,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-09", "versions": 1 @@ -110972,20 +126244,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "683e725f672b7d9b", @@ -111001,22 +126273,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111030,20 +126302,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e4dd39237df58884", @@ -111059,22 +126331,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111088,20 +126360,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fc7b14aafa0b421e", @@ -111117,22 +126389,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111146,20 +126418,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "b661fb850c4b4b01", @@ -111175,22 +126447,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111203,18 +126475,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "dae5d5e5df5c4dd7", @@ -111230,19 +126502,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111255,8 +126527,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "ca3f2d9554e9e1c8", @@ -111271,11 +126543,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-09", "versions": 1 @@ -111302,8 +126574,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -111330,8 +126602,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -111358,8 +126630,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-09", "versions": 1 @@ -111372,16 +126644,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "5edabfc62f58d8cf", @@ -111397,16 +126669,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111419,16 +126691,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d2e8a6b39fe88f4c", @@ -111444,16 +126716,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111466,16 +126738,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "45c0b677c4920d03", @@ -111491,16 +126763,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111513,16 +126785,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "96bd0007dceec123", @@ -111538,16 +126810,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111560,13 +126832,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -111582,19 +126854,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-09", "versions": 1 @@ -111607,13 +126879,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -111629,19 +126901,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-09", "versions": 1 @@ -111654,8 +126926,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "6cad14c78ec330ac", @@ -111668,8 +126940,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2023-11-09", "versions": 1 @@ -111682,8 +126954,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "3d0f92e7f63978b6", @@ -111709,15 +126981,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3c0af11dbeeee506", @@ -111732,13 +127004,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111750,19 +127022,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "fcbe12fc4eaae12e", @@ -111777,27 +127049,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111809,19 +127081,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "e899acc664c8b808", @@ -111836,27 +127108,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111868,19 +127140,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "de29cd965a2e93d3", @@ -111895,27 +127167,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111927,15 +127199,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "69edab5d6ad91556", @@ -111950,13 +127222,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-09", "versions": 1 @@ -111968,17 +127240,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "52b7524a3941885c", @@ -111993,15 +127265,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-09", "versions": 1 @@ -112013,17 +127285,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "5a16ff38eb80da82", @@ -112038,15 +127310,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-09", "versions": 1 @@ -112056,13 +127328,13 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", + "Sequence composition calculation", "Taxonomic classification" ], "edam_topic": [], @@ -112076,11 +127348,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "porechop", "kraken2", - "nanoplot", - "taxonomy_krona_chart", "fastp", + "taxonomy_krona_chart", + "nanoplot", + "porechop", "fastqc" ], "update_time": "2023-11-08", @@ -112091,13 +127363,13 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", + "Sequence composition calculation", "Taxonomic classification" ], "edam_topic": [], @@ -112111,11 +127383,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "porechop", "kraken2", - "nanoplot", - "taxonomy_krona_chart", "fastp", + "taxonomy_krona_chart", + "nanoplot", + "porechop", "fastqc" ], "update_time": "2023-11-08", @@ -112126,16 +127398,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "6f090b2c259847d2", @@ -112150,32 +127422,32 @@ "metagenomics" ], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_summary_single", + "mothur_cluster_split", + "mothur_count_seqs", "mothur_make_shared", "mothur_pre_cluster", - "mothur_summary_single", - "mothur_taxonomy_to_krona", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", - "mothur_align_seqs", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "XY_Plot_1" ], "update_time": "2023-11-06", @@ -112186,14 +127458,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Sequence alignment", "Sequence trimming", + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "26019c2b056d3a1c", @@ -112206,10 +127478,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rna_star", "multiqc", - "fastqc", "__FLATTEN__", + "fastqc", + "rna_star", "cutadapt" ], "update_time": "2023-11-06", @@ -112220,8 +127492,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "19fcce20ecaf2ef6", @@ -112235,14 +127507,14 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", "collection_element_identifiers", - "join1", - "Cut1", - "__TAG_FROM_FILE__", - "tp_replace_in_line", "Filter1", + "tp_replace_in_line", "deg_annotate", + "join1", + "__TAG_FROM_FILE__", + "Cut1", + "ggplot2_heatmap2", "deseq2" ], "update_time": "2023-11-06", @@ -112253,11 +127525,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -112271,8 +127543,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2023-11-06", "versions": 1 @@ -112305,8 +127577,8 @@ "edam_operation": [ "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "Sequence annotation" + "Sequence annotation", + "Sequence alignment" ], "edam_topic": [], "id": "2a7fbfc1c17e38bc", @@ -112319,9 +127591,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "hisat2", "gffread", "featurecounts", - "hisat2", "trimmomatic" ], "update_time": "2023-11-04", @@ -112332,13 +127604,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -112352,11 +127624,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2023-11-04", @@ -112367,14 +127639,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Sequence alignment", "Sequence trimming", + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Primer removal" ], "edam_topic": [], "id": "dc7f05cb5a62da77", @@ -112387,10 +127659,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rna_star", "multiqc", - "fastqc", "__FLATTEN__", + "fastqc", + "rna_star", "cutadapt" ], "update_time": "2023-11-03", @@ -112401,8 +127673,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "abf1aec0f3d48d03", @@ -112415,17 +127687,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_heatmap2", - "table_compute", "collection_element_identifiers", - "join1", - "Cut1", - "__TAG_FROM_FILE__", - "tp_replace_in_line", "Filter1", + "tp_replace_in_line", + "table_compute", + "tp_cat", "deg_annotate", - "deseq2", - "tp_cat" + "join1", + "__TAG_FROM_FILE__", + "Cut1", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2023-11-03", "versions": 0 @@ -112486,19 +127758,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "283bc048cc7a80f5", @@ -112514,20 +127786,20 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Cut1", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2023-10-26", "versions": 1 @@ -112537,13 +127809,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "RNA-Seq analysis", + "Statistical calculation", "Nucleic acid sequence analysis", + "Differential gene expression analysis", "Sequencing quality control", - "Differential gene expression analysis" + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "dcc7c5fdef8780fd", @@ -112556,20 +127828,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "htseq_count", + "bowtie2", "cat1", - "ggplot2_heatmap2", - "fastq_groomer", - "tp_sort_header_tool", + "Filter1", "collapse_dataset", - "tp_cut_tool", - "join1", - "Cut1", - "htseq_count", + "tp_sort_header_tool", "deg_annotate", + "join1", "fastqc", - "Filter1", - "bowtie2", - "deseq2" + "tp_cut_tool", + "Cut1", + "ggplot2_heatmap2", + "deseq2", + "fastq_groomer" ], "update_time": "2023-10-24", "versions": 8 @@ -112605,11 +127877,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Data handling" ], "edam_topic": [], "id": "0052e9b1b7bfec69", @@ -112622,12 +127894,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "fastq_dump", + "cufflinks", "samtools_sort", + "fastqc", "hisat2", - "cufflinks", - "fastqc" + "fastq_dump", + "cuffdiff" ], "update_time": "2023-10-19", "versions": 0 @@ -112640,8 +127912,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "0f6bb7847f8769af", @@ -112654,8 +127926,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2023-10-19", "versions": 5 @@ -112701,8 +127973,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bedtools_intersectbed", - "bedtools_subtractbed" + "bedtools_subtractbed", + "bedtools_intersectbed" ], "update_time": "2023-10-12", "versions": 2 @@ -112751,8 +128023,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bigwig_average", - "__APPLY_RULES__" + "__APPLY_RULES__", + "deeptools_bigwig_average" ], "update_time": "2023-10-05", "versions": 1 @@ -112764,19 +128036,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "b63d1e1024cc3295", @@ -112791,27 +128063,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-10-05", "versions": 1 @@ -112839,8 +128111,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-10-05", "versions": 1 @@ -112850,9 +128122,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "cf3f0760611f22f9", @@ -112865,8 +128137,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "featurecounts", "hisat2", + "featurecounts", "trimmomatic" ], "update_time": "2023-10-04", @@ -112877,10 +128149,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Validation", "Sequencing quality control", "Formatting", - "Validation" + "Data handling" ], "edam_topic": [], "id": "7e9269e78e989480", @@ -112895,10 +128167,10 @@ "transcriptomics" ], "tools": [ - "samtools_idxstats", - "picard_MarkDuplicates", + "rseqc_infer_experiment", "multiqc", - "rseqc_infer_experiment" + "samtools_idxstats", + "picard_MarkDuplicates" ], "update_time": "2023-10-02", "versions": 0 @@ -112921,8 +128193,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bigwig_average", - "__APPLY_RULES__" + "__APPLY_RULES__", + "deeptools_bigwig_average" ], "update_time": "2023-09-28", "versions": 1 @@ -112948,8 +128220,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "repeatmasker_wrapper", - "repeatmodeler" + "repeatmodeler", + "repeatmasker_wrapper" ], "update_time": "2023-09-28", "versions": 1 @@ -112961,19 +128233,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "8a215695e7b57cf5", @@ -112988,27 +128260,27 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "__APPLY_RULES__", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", - "__APPLY_RULES__", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-09-28", "versions": 1 @@ -113018,12 +128290,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", "Sequence contamination filtering", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequencing quality control", - "Formatting" + "Formatting", + "Data handling" ], "edam_topic": [], "id": "98286b6154e1b57f", @@ -113037,14 +128309,14 @@ "tags": [], "tools": [ "picard_NormalizeFasta", - "fastq_dump", - "rbc_mirdeep2_mapper", - "rbc_mirdeep2", - "fastp", - "cshl_fastx_collapser", "fastqc", + "cshl_fastx_collapser", + "fastp", "rbc_mirdeep2_quantifier", - "CONVERTER_gz_to_uncompressed" + "rbc_mirdeep2", + "rbc_mirdeep2_mapper", + "CONVERTER_gz_to_uncompressed", + "fastq_dump" ], "update_time": "2023-09-26", "versions": 0 @@ -113094,8 +128366,8 @@ "bga23" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-09-21", "versions": 2 @@ -113120,9 +128392,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-21", @@ -113135,15 +128407,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "53fdff74729a6780", @@ -113158,18 +128430,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -113181,14 +128453,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "2f774500d5bec9a6", @@ -113203,14 +128475,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -113222,15 +128494,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "3e6c9ab5ef3250ae", @@ -113245,17 +128517,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -113267,14 +128539,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "63b3b266bde77563", @@ -113289,14 +128561,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2023-09-21", "versions": 1 @@ -113322,24 +128594,24 @@ "name:singlecell" ], "tools": [ - "anndata_inspect", + "scanpy_run_tsne", + "scanpy_find_cluster", "scanpy_plot", - "anndata_manipulate", - "anndata_ops", - "join1", "scanpy_compute_graph", - "Cut1", + "anndata_manipulate", "scanpy_plot_embed", - "scanpy_run_tsne", + "anndata_ops", "scanpy_run_umap", - "scanpy_run_pca", "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_normalise_data", - "scanpy_find_cluster", + "scanpy_run_pca", + "scanpy_filter_genes", "scanpy_scale_data", + "join1", + "scanpy_find_variable_genes", "scanpy_filter_cells", - "scanpy_filter_genes" + "Cut1", + "anndata_inspect", + "scanpy_normalise_data" ], "update_time": "2023-09-20", "versions": 1 @@ -113373,13 +128645,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "RNA-Seq analysis", - "Differential gene expression analysis", "Sequence alignment", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "dab54002b3c0e351", @@ -113394,12 +128666,12 @@ "cpb" ], "tools": [ - "featurecounts", "Filter1", - "hisat2", + "featurecounts", "collection_column_join", - "deseq2", - "bamFilter" + "bamFilter", + "hisat2", + "deseq2" ], "update_time": "2023-09-14", "versions": 5 @@ -113455,8 +128727,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-09-14", "versions": 1 @@ -113470,10 +128742,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "23468eea382e6bb4", @@ -113488,20 +128760,20 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "wc_gnu", - "Cut1", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", + "__EXTRACT_DATASET__", + "wc_gnu", + "collapse_dataset", + "deeptools_bigwig_average", "multiqc", + "table_compute", + "bedtools_intersectbed", "random_lines1", - "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "tp_sorted_uniq", + "Cut1" ], "update_time": "2023-09-07", "versions": 1 @@ -113515,10 +128787,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6dcb43f86b9cd7dc", @@ -113533,19 +128805,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-09-07", "versions": 1 @@ -113559,10 +128831,10 @@ "edam_operation": [ "Peak calling", "Gene regulatory network analysis", - "Mapping", - "Enrichment analysis", + "Validation", "Sequencing quality control", - "Validation" + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6a2dace98986992a", @@ -113577,19 +128849,19 @@ "chip" ], "tools": [ - "__EXTRACT_DATASET__", - "table_compute", - "collapse_dataset", - "Cut1", - "samtools_view", + "macs2_callpeak", + "wig_to_bigWig", "param_value_from_file", - "tp_sorted_uniq", "Filter1", - "wig_to_bigWig", - "multiqc", + "__EXTRACT_DATASET__", "deeptools_bigwig_average", - "macs2_callpeak", - "bedtools_intersectbed" + "collapse_dataset", + "multiqc", + "table_compute", + "bedtools_intersectbed", + "tp_sorted_uniq", + "Cut1", + "samtools_view" ], "update_time": "2023-09-07", "versions": 1 @@ -113614,9 +128886,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-09-07", "versions": 1 @@ -113641,9 +128913,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-07", @@ -113669,9 +128941,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-09-07", "versions": 1 @@ -113700,8 +128972,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-09-07", @@ -113756,9 +129028,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-09-07", @@ -113788,8 +129060,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-09-07", @@ -113831,15 +129103,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "90ed607bedd65524", @@ -113854,13 +129126,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -113872,19 +129144,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Formatting", - "Sequencing quality control", - "Gene regulatory network analysis", + "Mapping", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "b5e8f4a0ff226921", @@ -113899,26 +129171,26 @@ "atacseq" ], "tools": [ + "wig_to_bigWig", + "pe_histogram", "bedtools_bamtobed", - "bedtools_slopbed", - "samtools_view", "tp_grep_tool", - "wig_to_bigWig", + "bowtie2", + "param_value_from_file", + "Add_a_column1", "samtools_idxstats", "deeptools_bigwig_average", + "multiqc", "bamFilter", + "cutadapt", + "samtools_view", + "picard_MarkDuplicates", "macs2_callpeak", - "Add_a_column1", - "param_value_from_file", "cat1", - "picard_MarkDuplicates", - "tp_awk_tool", - "pe_histogram", - "multiqc", - "bowtie2", "bedtools_coveragebed", - "cutadapt", - "bedtools_mergebed" + "bedtools_mergebed", + "bedtools_slopbed", + "tp_awk_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -113930,15 +129202,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "cb011900fc0ee12a", @@ -113953,13 +129225,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -113971,17 +129243,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "67992bf894a82587", @@ -113996,15 +129268,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-09-07", "versions": 1 @@ -114032,8 +129304,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-09-07", "versions": 1 @@ -114044,8 +129316,8 @@ "doi": "", "edam_operation": [ "Sequencing quality control", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequence trimming" ], "edam_topic": [], @@ -114059,8 +129331,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "sickle" + "sickle", + "fastqc" ], "update_time": "2023-09-02", "versions": 22 @@ -114070,11 +129342,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", - "Sequence alignment" + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "efb10012b8448b21", @@ -114087,14 +129359,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "htseq_count", - "samtools_sort", "samtools_stats", - "samtool_filter2", - "hisat2", "cufflinks", - "fastqc" + "samtool_filter2", + "trimmomatic", + "samtools_sort", + "fastqc", + "hisat2" ], "update_time": "2023-08-29", "versions": 1 @@ -114107,9 +129379,9 @@ ], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "a2a924b871b1c96d", @@ -114126,15 +129398,15 @@ "name:training" ], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2023-08-24", "versions": 1 @@ -114144,9 +129416,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "58a91a914e381dcf", @@ -114159,8 +129431,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-08-22", "versions": 0 @@ -114183,11 +129455,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-08-18", "versions": 0 @@ -114197,9 +129469,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "cd3bce36b6ef073d", @@ -114212,8 +129484,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-08-16", "versions": 1 @@ -114224,9 +129496,9 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", "Phylogenetic tree generation", - "Genome visualisation" + "Genome visualisation", + "Variant calling" ], "edam_topic": [], "id": "5674956f5c18b85b", @@ -114250,9 +129522,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0555313573cd1ee2", @@ -114265,8 +129537,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-08-04", "versions": 0 @@ -114276,10 +129548,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence alignment", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "037c3a9d872be3de", @@ -114292,10 +129564,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "samtools_sort", "hisat2", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2023-08-01", "versions": 9 @@ -114308,9 +129580,9 @@ ], "doi": "", "edam_operation": [ - "Gene expression analysis", + "RNA-Seq quantification", "Sequence composition calculation", - "RNA-Seq quantification" + "Gene expression analysis" ], "edam_topic": [], "id": "1fe6b25825d9b736", @@ -114327,15 +129599,15 @@ "name:training" ], "tools": [ - "join1", - "Cut1", + "_dropletBarcodePlot", "dropletutils_read_10x", "_ensembl_gtf2gene_list", "sceasy_convert", - "dropletutils_empty_drops", - "alevin", "_salmon_kallisto_mtx_to_10x", - "_dropletBarcodePlot" + "alevin", + "join1", + "Cut1", + "dropletutils_empty_drops" ], "update_time": "2023-07-18", "versions": 0 @@ -114345,15 +129617,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Genome visualisation", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Validation" + "Validation", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "5efe288b18c7d0ab", @@ -114368,12 +129640,12 @@ "sequence-analysis" ], "tools": [ - "trim_galore", + "bowtie2", "samtools_stats", "multiqc", - "jbrowse", + "trim_galore", "fastqc", - "bowtie2" + "jbrowse" ], "update_time": "2023-07-16", "versions": 0 @@ -114385,10 +129657,10 @@ "edam_operation": [ "Pairwise sequence alignment", "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "63adc811e3ae529d", @@ -114401,15 +129673,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", + "cshl_fastq_quality_filter", "EMBOSS: transeq101", + "minimap2", + "fastq_to_fasta_python", "bioext_bealign", - "tp_sed_tool", "bioext_bam2msa", - "cshl_fastq_quality_filter", - "minimap2", "cshl_fasta_formatter", - "fastq_to_fasta_python" + "tp_sed_tool", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2023-07-10", "versions": 44 @@ -114430,11 +129702,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "tp_cat", "tp_sort_header_tool", - "tp_awk_tool", - "tp_grep_tool", "tp_uniq_tool", - "tp_cat" + "tp_grep_tool", + "tp_awk_tool" ], "update_time": "2023-07-06", "versions": 6 @@ -114444,14 +129716,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Statistical calculation", - "Sequence composition calculation", - "Read mapping", + "Generation", "Genome indexing", - "Sequencing quality control", + "Sequence composition calculation", + "Statistical calculation", "Sequence alignment", - "Generation" + "Sequencing quality control", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "c9a8fd89224e7414", @@ -114466,9 +129738,9 @@ "sequence-analysis" ], "tools": [ - "fastqc", + "jbrowse", "bwa_mem", - "jbrowse" + "fastqc" ], "update_time": "2023-07-01", "versions": 2 @@ -114478,14 +129750,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Statistical calculation", - "Sequence composition calculation", - "Read mapping", + "Generation", "Genome indexing", - "Sequencing quality control", + "Sequence composition calculation", + "Statistical calculation", "Sequence alignment", - "Generation" + "Sequencing quality control", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "53d65fd38b9b8c1b", @@ -114498,9 +129770,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "jbrowse", "bwa_mem", - "jbrowse" + "fastqc" ], "update_time": "2023-06-29", "versions": 3 @@ -114513,10 +129785,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "4884918895db9af0", @@ -114529,11 +129801,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "filter_by_fasta_ids", "EMBOSS: transeq101", - "tp_sed_tool", "bioext_bam2msa", - "cshl_fasta_formatter" + "cshl_fasta_formatter", + "tp_sed_tool", + "filter_by_fasta_ids" ], "update_time": "2023-06-22", "versions": 2 @@ -114554,18 +129826,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gmx_energy", - "ambertools_acpype", - "gmx_editconf", - "md_converter", - "get_pdb", "gmx_solvate", - "tp_grep_tool", - "gmx_sim", + "gmx_setup", "gmx_merge_topology_files", + "ambertools_acpype", + "get_pdb", "openbabel_compound_convert", "gmx_em", - "gmx_setup" + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_energy", + "gmx_sim" ], "update_time": "2023-06-20", "versions": 1 @@ -114598,9 +129870,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "544ce8ff6c9f6d4c", @@ -114613,8 +129885,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "featurecounts", "hisat2", + "featurecounts", "trimmomatic" ], "update_time": "2023-06-05", @@ -114627,14 +129899,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "9fc9f1db50019929", @@ -114653,22 +129925,22 @@ "name:v2.1.0+galaxy3" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2023-05-30", "versions": 2 @@ -114678,19 +129950,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Differential gene expression analysis", - "Read summarisation", "Statistical calculation", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9e74e3455e47c813", @@ -114703,14 +129975,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "__FLATTEN__", + "bowtie2", "featurecounts", - "fasterq_dump", "multiqc", + "fasterq_dump", + "__FLATTEN__", "fastqc", - "deseq2", - "bowtie2", - "cutadapt" + "cutadapt", + "deseq2" ], "update_time": "2023-05-24", "versions": 0 @@ -114720,12 +129992,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", "De-novo assembly", + "Sequence composition calculation", + "Statistical calculation", + "Genome assembly", "Mapping assembly", "Sequencing quality control", - "Genome assembly", "Cross-assembly" ], "edam_topic": [], @@ -114739,9 +130011,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "porechop", "flye", - "porechop" + "fastqc" ], "update_time": "2023-05-22", "versions": 2 @@ -114751,16 +130023,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Sequence alignment", - "Gene regulatory network analysis", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", + "Gene regulatory network analysis", "Read pre-processing", - "Sequence trimming" + "Sequence trimming", + "Enrichment analysis" ], "edam_topic": [], "id": "8e32b0a5a141543e", @@ -114779,8 +130051,8 @@ "tools": [ "fastqc", "macs2_callpeak", - "trim_galore", - "hisat2" + "hisat2", + "trim_galore" ], "update_time": "2023-05-21", "versions": 28 @@ -114790,18 +130062,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ac8b74b911778fbc", @@ -114815,11 +130087,11 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "fasterq_dump", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-17", "versions": 0 @@ -114829,17 +130101,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", + "Data handling", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "734e08331f8f34b7", @@ -114853,24 +130125,24 @@ "tags": [], "tools": [ "gprofiler_gost", - "trim_galore", - "salmon", + "tp_find_and_replace", + "tp_tail_tool", + "collection_column_join", + "join1", "fastqc", - "column_order_header_sort", - "fastq_groomer", + "Filter1", + "fasterq_dump", "gffread", - "tp_cut_tool", - "tp_find_and_replace", + "trim_galore", + "column_order_header_sort", + "tp_replace_in_column", "limma_voom", + "salmon", "melt", - "join1", - "tp_replace_in_column", - "tp_tail_tool", - "Cut1", - "fasterq_dump", "Remove beginning1", - "collection_column_join", - "Filter1" + "tp_cut_tool", + "Cut1", + "fastq_groomer" ], "update_time": "2023-05-15", "versions": 2 @@ -114891,8 +130163,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_sort_header_tool", "gops_join_1", + "tp_sort_header_tool", "Grouping1" ], "update_time": "2023-05-10", @@ -114903,17 +130175,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "aac2ae0419f7d515", @@ -114928,13 +130200,13 @@ "tools": [ "limma_voom", "gffread", - "tp_cut_tool", - "trim_galore", - "fasterq_dump", "salmon", + "fasterq_dump", + "trim_galore", + "column_order_header_sort", "collection_column_join", "fastqc", - "column_order_header_sort" + "tp_cut_tool" ], "update_time": "2023-05-03", "versions": 1 @@ -114944,17 +130216,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "a89def2c2462674a", @@ -114969,13 +130241,13 @@ "tools": [ "limma_voom", "gffread", - "tp_cut_tool", - "trim_galore", - "fasterq_dump", "salmon", + "fasterq_dump", + "trim_galore", + "column_order_header_sort", "collection_column_join", "fastqc", - "column_order_header_sort" + "tp_cut_tool" ], "update_time": "2023-05-01", "versions": 1 @@ -114985,17 +130257,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "93650de42fb8c015", @@ -115010,13 +130282,13 @@ "tools": [ "limma_voom", "gffread", - "tp_cut_tool", - "trim_galore", - "fasterq_dump", "salmon", + "fasterq_dump", + "trim_galore", + "column_order_header_sort", "collection_column_join", "fastqc", - "column_order_header_sort" + "tp_cut_tool" ], "update_time": "2023-05-01", "versions": 0 @@ -115026,10 +130298,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Enrichment analysis", "Peak calling", - "Gene regulatory network analysis" + "Gene regulatory network analysis", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "59d34b4f0178120b", @@ -115042,15 +130314,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_plot_heatmap", - "deeptools_multi_bam_summary", - "deeptools_plot_fingerprint", - "bedtools_getfastabed", "deeptools_plot_correlation", - "idr", + "macs2_callpeak", + "deeptools_multi_bam_summary", "meme_chip", + "deeptools_plot_heatmap", + "deeptools_plot_fingerprint", "deeptools_compute_matrix", - "macs2_callpeak" + "idr", + "bedtools_getfastabed" ], "update_time": "2023-04-25", "versions": 4 @@ -115060,9 +130332,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "58ceaed0a42fe60a", @@ -115075,8 +130347,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-04-18", "versions": 0 @@ -115086,14 +130358,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", - "Differential gene expression analysis", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", + "Differential gene expression analysis", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0930f955bdac93e8", @@ -115106,12 +130378,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "volcanoplot", - "salmon", + "Filter1", "__MERGE_COLLECTION__", + "salmon", "multiqc", + "volcanoplot", "fastqc", - "Filter1", "deseq2" ], "update_time": "2023-04-05", @@ -115135,13 +130407,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2023-03-27", "versions": 2 @@ -115152,8 +130424,8 @@ "doi": "", "edam_operation": [ "Read mapping", - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d72e33effe07de02", @@ -115166,12 +130438,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "cufflinks", - "deseq2", "bowtie2", - "cuffmerge" + "cufflinks", + "tophat2", + "cuffmerge", + "cuffdiff", + "deseq2" ], "update_time": "2023-03-27", "versions": 2 @@ -115194,13 +130466,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2023-03-24", "versions": 4 @@ -115210,13 +130482,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", + "Read mapping", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "2ceff2cf26eae4cd", @@ -115229,22 +130501,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", + "samtools_idxstats", + "sort1", + "Filter1", "vcffilter2", - "Summary_Statistics1", "snpsift_vartype", - "freebayes", - "samtool_filter2", - "sort1", + "bam_to_sam", + "Summary_Statistics1", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-03-24", "versions": 1 @@ -115254,16 +130526,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "26c4909f2f3df704", @@ -115277,21 +130549,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", + "samtools_idxstats", + "sort1", + "Filter1", "vcffilter2", - "Summary_Statistics1", "snpsift_vartype", - "freebayes", - "samtool_filter2", - "sort1", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-03-24", "versions": 0 @@ -115314,13 +130586,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2023-03-22", "versions": 3 @@ -115343,11 +130615,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "tp_head_tool", + "bedtools_intersectbed", "tp_sort_header_tool", "comp1", - "datamash_ops", - "tp_head_tool", - "bedtools_intersectbed" + "datamash_ops" ], "update_time": "2023-03-06", "versions": 1 @@ -115370,11 +130642,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "spring_model_all", - "__FILTER_FAILED_DATASETS__", - "hhsearch", "collection_element_identifiers", "rbc_splitfasta", + "__FILTER_FAILED_DATASETS__", + "hhsearch", + "spring_model_all", "ffindex_dbkit_create", "spring_minz" ], @@ -115386,13 +130658,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "b2f3d7e4cd4d0f11", @@ -115406,12 +130678,12 @@ "tags": [], "tools": [ "mothur_screen_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_filter_seqs", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_count_seqs", + "mothur_unique_seqs" ], "update_time": "2023-02-28", "versions": 1 @@ -115423,16 +130695,16 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence trimming", + "Read mapping" ], "edam_topic": [], "id": "18c6e87a884fb5ed", @@ -115445,13 +130717,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "varscan_mpileup", "samtools_mpileup", - "trim_galore", "snpEff", - "fastqc", - "snpSift_annotate" + "snpSift_annotate", + "varscan_mpileup", + "trim_galore", + "bwa_mem", + "fastqc" ], "update_time": "2023-02-27", "versions": 25 @@ -115464,11 +130736,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "badd4b56dbdeaba7", @@ -115485,9 +130757,9 @@ ], "tools": [ "kraken2", - "porechop", "fastp", "multiqc", + "porechop", "collection_column_join", "fastqc" ], @@ -115512,9 +130784,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_to_fasta_python", + "fasta_merge_files_and_filter_unique_sequences", "fasterq_dump", - "fasta_merge_files_and_filter_unique_sequences" + "fastq_to_fasta_python" ], "update_time": "2023-02-23", "versions": 0 @@ -115539,9 +130811,9 @@ "hi-c" ], "tools": [ - "Filter1", - "hicup2juicer", "compose_text_param", + "hicup2juicer", + "Filter1", "hicup_hicup" ], "update_time": "2023-02-23", @@ -115567,9 +130839,9 @@ "hi-c" ], "tools": [ + "cooler_cload_tabix", "cooler_makebins", - "cooler_balance", - "cooler_cload_tabix" + "cooler_balance" ], "update_time": "2023-02-23", "versions": 1 @@ -115598,8 +130870,8 @@ ], "tools": [ "cooler_csort_tabix", - "Filter1", "compose_text_param", + "Filter1", "pygenomeTracks" ], "update_time": "2023-02-23", @@ -115641,17 +130913,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "842c09b49c456429", @@ -115666,15 +130938,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-02-23", "versions": 1 @@ -115700,10 +130972,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", "hisat2", - "picard_MarkDuplicates", - "picard_AddOrReplaceReadGroups" + "samtools_view", + "picard_AddOrReplaceReadGroups", + "picard_MarkDuplicates" ], "update_time": "2023-02-19", "versions": 2 @@ -115729,10 +131001,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_view", "hisat2", - "picard_MarkDuplicates", - "picard_AddOrReplaceReadGroups" + "samtools_view", + "picard_AddOrReplaceReadGroups", + "picard_MarkDuplicates" ], "update_time": "2023-02-19", "versions": 18 @@ -115742,14 +131014,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Primer removal", "Read pre-processing", + "Validation", + "Sequence alignment", "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "Primer removal" ], "edam_topic": [], "id": "8ebcae16a7822d93", @@ -115762,10 +131034,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_sort_header_tool", - "rna_star", "featurecounts", "multiqc", + "tp_sort_header_tool", + "rna_star", "cutadapt" ], "update_time": "2023-02-04", @@ -115776,15 +131048,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", "Statistical calculation", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", - "Validation" + "Validation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6dada297572d77bd", @@ -115797,10 +131069,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "sailfish", - "trim_galore", "multiqc", + "trim_galore", + "sailfish", + "fastqc", "deseq2" ], "update_time": "2023-01-31", @@ -115811,13 +131083,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "271b97e5c00c4da4", @@ -115830,12 +131102,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", + "trimmomatic", "multiqc", - "hisat2", + "__FLATTEN__", "fastqc", - "__FLATTEN__" + "hisat2" ], "update_time": "2023-01-30", "versions": 1 @@ -115845,15 +131117,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "Validation" + "Validation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "53834a5fb46ca0f6", @@ -115866,9 +131138,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sailfish", - "trim_galore", "multiqc", + "trim_galore", + "sailfish", "fastqc", "deseq2" ], @@ -115880,16 +131152,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4054ceeba1a2fa69", @@ -115902,22 +131174,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "bedtools_coveragebed", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "samtools_idxstats", + "snpEff", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-24", "versions": 0 @@ -115927,16 +131199,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "6a08af55c086ec62", @@ -115950,19 +131222,19 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "tp_sort_header_tool", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "freebayes", "vcffilter2", - "picard_MarkDuplicatesWithMateCigar", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "picard_MarkDuplicatesWithMateCigar", + "samtools_flagstat" ], "update_time": "2023-01-24", "versions": 0 @@ -115974,15 +131246,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "778a8867b0a6ea4f", @@ -115997,18 +131269,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -116020,15 +131292,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "1f28e673ea725541", @@ -116043,18 +131315,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -116066,15 +131338,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "63f61ad7cae40646", @@ -116089,13 +131361,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -116107,15 +131379,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "c74e3a24751d9924", @@ -116130,17 +131402,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -116152,19 +131424,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e42a07b777c9f9dc", @@ -116179,23 +131451,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -116207,15 +131479,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7cee34a6c06c21e4", @@ -116230,13 +131502,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -116248,19 +131520,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "d4029ce1344e874a", @@ -116275,23 +131547,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -116304,21 +131576,21 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Mapping", + "Statistical calculation", "Differential gene expression analysis", - "Variant calling", - "RNA-Seq analysis", - "Read summarisation", "Primer removal", + "Sequencing quality control", + "Variant calling", + "Sequence composition calculation", "Read pre-processing", - "Sequence trimming", - "Mapping", - "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "eb4b32fcf4a9f64a", @@ -116331,29 +131603,29 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gatk4_mutect2", + "bcftools_cnv", + "trimmomatic", + "cshl_fastq_quality_boxplot", + "rseqc_tin", "bedtools_bamtobed", - "rseqc_read_distribution", - "trim_galore", - "samtools_view", - "vcfcheck", - "samtools_sort", "fastqc", - "cshl_fastq_quality_boxplot", + "bowtie2", + "featurecounts", + "gatk4_mutect2", + "samtools_sort", + "multiqc", + "vcfcheck", + "deg_annotate", + "samtools_view", + "deseq2", + "samtools_flagstat", "fastq_stats", - "rseqc_tin", + "trim_galore", + "rseqc_read_distribution", "freebayes", - "deseq2", "vcfgeno2haplo", - "featurecounts", - "samtools_markdup", - "samtools_flagstat", - "trimmomatic", - "bcftools_cnv", "fastq_info", - "deg_annotate", - "multiqc", - "bowtie2" + "samtools_markdup" ], "update_time": "2023-01-12", "versions": 7 @@ -116363,9 +131635,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "8ed3444a692f8e61", @@ -116378,9 +131650,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "fastq_join", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2023-01-12", "versions": 0 @@ -116390,16 +131662,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e6f57346a02be07f", @@ -116413,19 +131685,19 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-10", "versions": 0 @@ -116435,15 +131707,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Statistical calculation", "Differential gene expression analysis", - "Sequencing quality control", "Sequence alignment", - "Read summarisation", - "Statistical calculation", + "Sequencing quality control", "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence composition calculation", + "RNA-Seq quantification", + "Read summarisation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d761637d43ee0324", @@ -116457,13 +131729,13 @@ "tags": [], "tools": [ "edger", - "trimmomatic", - "samtools_view", "featurecounts", - "hisat2", + "trimmomatic", "fastqc", - "deseq2", - "stringtie" + "stringtie", + "hisat2", + "samtools_view", + "deseq2" ], "update_time": "2023-01-10", "versions": 1 @@ -116473,16 +131745,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "6d8f0be547b12528", @@ -116496,22 +131768,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", "snpEff_download", - "tp_sort_header_tool", + "freebayes", + "snpEff", "vcffilter2", - "Summary_Statistics1", "bcftools_plugin_counts", - "snpEff", - "freebayes", - "samtool_filter2", + "bam_to_sam", + "tp_sort_header_tool", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-09", "versions": 0 @@ -116521,16 +131793,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "78979ec454b98338", @@ -116543,22 +131815,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", - "Summary_Statistics1", "bcftools_plugin_counts", - "freebayes", - "samtool_filter2", + "bam_to_sam", + "tp_sort_header_tool", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-09", "versions": 0 @@ -116568,16 +131840,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ab6e4277fc825c5d", @@ -116590,24 +131862,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", "snpEff_download", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", + "snpEff", "vcffilter2", - "Summary_Statistics1", "bcftools_plugin_counts", - "snpEff", - "freebayes", - "samtool_filter2", + "bam_to_sam", + "tp_sort_header_tool", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-09", "versions": 0 @@ -116617,16 +131889,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "7decdde67868ed0f", @@ -116639,25 +131911,25 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", + "snpEff_databases", "fastqc", + "bowtie2", + "Filter1", "samtools_idxstats", - "bam_to_sam", "vcffilter2", - "freebayes", - "snpEff_databases", "tp_sort_header_tool", - "snpEff_download", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bowtie2", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2023-01-08", "versions": 0 @@ -116667,16 +131939,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "1deaf458d6d8695a", @@ -116689,24 +131961,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "snpEff_databases", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", "snpEff_download", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", + "snpEff", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "snpEff_databases", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bwa_mem", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-07", "versions": 0 @@ -116716,13 +131988,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", + "Read mapping", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "de2861cdbd4e29ce", @@ -116735,27 +132007,27 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", "snpSift_extractFields", - "snpsift_vartype", + "trimmomatic", + "snpEff_databases", "fastqc", + "bowtie2", + "Filter1", "samtools_idxstats", - "bam_to_sam", "vcffilter2", - "freebayes", - "snpSift_filter", - "snpEff_databases", "tp_sort_header_tool", - "snpEff_download", - "snpEff", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "snpsift_vartype", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bowtie2", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes", + "snpSift_filter" ], "update_time": "2023-01-06", "versions": 4 @@ -116765,16 +132037,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8b08a05c5926dd0f", @@ -116787,27 +132059,27 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", "snpSift_extractFields", - "snpsift_vartype", + "trimmomatic", + "snpEff_databases", "fastqc", + "Filter1", "samtools_idxstats", - "bam_to_sam", "vcffilter2", - "freebayes", - "snpSift_filter", - "snpEff_databases", "tp_sort_header_tool", - "snpEff_download", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "snpsift_vartype", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes", + "snpSift_filter" ], "update_time": "2023-01-06", "versions": 12 @@ -116817,16 +132089,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "692a2b0bb818336d", @@ -116839,22 +132111,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -116864,16 +132136,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "41bbf3cd893d400a", @@ -116886,24 +132158,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -116913,16 +132185,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d0981820adf9c7d2", @@ -116935,22 +132207,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -116960,16 +132232,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "c4aaf11b0cb6e5ac", @@ -116982,24 +132254,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -117009,16 +132281,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "a4f7af1e2cd826c3", @@ -117031,24 +132303,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -117058,16 +132330,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f63f7a0a33a83841", @@ -117080,24 +132352,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-05", "versions": 0 @@ -117107,16 +132379,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "21a047a4e068860f", @@ -117129,23 +132401,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "bedtools_coveragebed", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-04", "versions": 0 @@ -117155,16 +132427,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d314df52f2f51502", @@ -117177,22 +132449,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-04", "versions": 0 @@ -117202,16 +132474,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8c1516493c55bf7d", @@ -117224,24 +132496,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-04", "versions": 0 @@ -117251,14 +132523,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", "Gene prediction", + "Coding region prediction", "Genome annotation", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Genome assembly", - "Coding region prediction", - "Sequencing quality control" + "Sequencing quality control", + "Aggregation" ], "edam_topic": [], "id": "b43b72dcf5f7694d", @@ -117271,11 +132543,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "prokka", + "unicycler", "trimmomatic", "export_remote", - "prokka", - "fastqc", - "unicycler" + "fastqc" ], "update_time": "2023-01-03", "versions": 9 @@ -117285,16 +132557,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "28abac549697f65a", @@ -117307,24 +132579,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-03", "versions": 0 @@ -117334,16 +132606,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f0feca8af9aeddba", @@ -117357,22 +132629,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-03", "versions": 0 @@ -117382,16 +132654,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "89660361d4121fa8", @@ -117405,21 +132677,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-02", "versions": 0 @@ -117429,16 +132701,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8b133c1d302c8681", @@ -117452,20 +132724,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-02", "versions": 0 @@ -117475,16 +132747,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d196c3bde666eccb", @@ -117497,23 +132769,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "bedtools_coveragebed", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-02", "versions": 0 @@ -117523,16 +132795,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4d0607d3589e0775", @@ -117545,23 +132817,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117571,16 +132843,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "02c96a9c6bb708ac", @@ -117593,22 +132865,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117618,16 +132890,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2e65bc5f9d9f2a75", @@ -117640,23 +132912,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117666,16 +132938,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f302d673420a9bdd", @@ -117688,23 +132960,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117714,16 +132986,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "86b802ea75d18160", @@ -117736,22 +133008,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", "bcftools_stats", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117761,16 +133033,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ced446bf2428497b", @@ -117783,22 +133055,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117808,16 +133080,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "39e79458c9ba581c", @@ -117830,21 +133102,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117854,16 +133126,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d2edc47cc7963885", @@ -117876,21 +133148,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117900,16 +133172,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "a98a3ac1a41752bc", @@ -117922,22 +133194,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117947,16 +133219,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f9d546aae406cf15", @@ -117969,23 +133241,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "bedtools_coveragebed", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -117995,16 +133267,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "262ab42118016c41", @@ -118017,22 +133289,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -118042,16 +133314,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b461ac6f18e0c9cf", @@ -118064,23 +133336,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", + "bedtools_coveragebed", + "freebayes", + "sort1", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "Filter1", - "bowtie2", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -118090,16 +133362,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ba405b449e27ba37", @@ -118112,22 +133384,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -118137,16 +133409,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b8804291f2754fc8", @@ -118160,20 +133432,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", + "snpEff", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -118183,16 +133455,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "3dc57709c4387ba7", @@ -118206,19 +133478,19 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2023-01-01", "versions": 0 @@ -118228,10 +133500,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Data handling", + "Sequencing quality control" ], "edam_topic": [], "id": "0a3513961f0cf9dd", @@ -118244,9 +133516,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "fasterq_dump", "trimmer", - "fasterq_dump" + "fastqc" ], "update_time": "2022-12-28", "versions": 1 @@ -118256,17 +133528,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "427fce51fd9508eb", @@ -118280,16 +133552,16 @@ "tags": [], "tools": [ "limma_voom", - "Show tail1", "gffread", - "Cut1", - "trim_galore", - "fasterq_dump", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "Grep1" + "Cut1", + "__RELABEL_FROM_FILE__", + "Show tail1" ], "update_time": "2022-12-28", "versions": 7 @@ -118299,17 +133571,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "228ae7f537a60226", @@ -118324,14 +133596,14 @@ "tools": [ "limma_voom", "gffread", - "Cut1", - "trim_galore", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "tp_tail_tool" + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2022-12-28", "versions": 4 @@ -118341,16 +133613,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "46e4acdc08eb3ea5", @@ -118363,24 +133635,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "snpSift_annotate", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "Summary_Statistics1", - "snpEff", + "bedtools_coveragebed", "freebayes", - "samtool_filter2", "sort1", + "snpSift_annotate", + "vcffilter2", + "snpEff", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", "snpSift_filter", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-12-27", "versions": 0 @@ -118390,13 +133662,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Sequence trimming", + "Primer removal", + "Read mapping" ], "edam_topic": [], "id": "7b9f36ae2174164a", @@ -118409,11 +133681,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa", - "samtools_view", + "cutadapt", "bcftools_call", "bcftools_mpileup", - "cutadapt" + "bwa", + "samtools_view" ], "update_time": "2022-12-22", "versions": 12 @@ -118423,9 +133695,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0d6a4dfbccafd2a2", @@ -118438,8 +133710,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2022-12-12", "versions": 1 @@ -118449,19 +133721,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Validation", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Annotation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", + "Validation", "Sequence trimming", - "Annotation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "5944c5effd56b0d6", @@ -118474,18 +133746,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "rseqc_geneBody_coverage", "limma_voom", - "volcanoplot", - "Cut1", "featurecounts", + "cutadapt", + "multiqc", "fasterq_dump", - "hisat2", + "volcanoplot", "annotatemyids", - "rseqc_geneBody_coverage", "collection_column_join", - "multiqc", - "cutadapt" + "fastqc", + "hisat2", + "Cut1" ], "update_time": "2022-12-08", "versions": 0 @@ -118497,15 +133769,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "93e69c7e7a857ca3", @@ -118520,18 +133792,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -118543,15 +133815,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "676b88d0aac13fa5", @@ -118566,17 +133838,17 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -118588,15 +133860,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "3fc5bdbd6355477c", @@ -118611,13 +133883,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -118629,19 +133901,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "907aaf55487ddf43", @@ -118656,23 +133928,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -118684,15 +133956,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e12296df7cf33c69", @@ -118707,13 +133979,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -118725,17 +133997,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c156e67ad1ae4a97", @@ -118750,15 +134022,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -118781,11 +134053,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-11-30", "versions": 1 @@ -118795,13 +134067,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "7a203cf1678df56d", @@ -118814,11 +134086,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 3 @@ -118842,14 +134114,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2022-11-30", "versions": 5 @@ -118859,13 +134131,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "30883502ec515fe2", @@ -118878,11 +134150,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 4 @@ -118892,13 +134164,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "63d590e8567f7157", @@ -118911,11 +134183,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 2 @@ -118925,13 +134197,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "e5a01f746bc9e9b5", @@ -118944,11 +134216,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 1 @@ -118958,13 +134230,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "75f14618020c922a", @@ -118977,11 +134249,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 1 @@ -118991,13 +134263,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "13460c791ca97689", @@ -119010,11 +134282,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 1 @@ -119024,13 +134296,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "f961fc46d4fddecc", @@ -119043,11 +134315,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-30", "versions": 1 @@ -119078,16 +134350,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5ffeb9904cf5f0bf", @@ -119100,21 +134372,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "bedtools_coveragebed", + "freebayes", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-11-25", "versions": 0 @@ -119124,13 +134396,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "2375a915a5b33b39", @@ -119143,11 +134415,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-11-23", "versions": 1 @@ -119157,11 +134429,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping" ], "edam_topic": [], "id": "3e2bbafb8c6580af", @@ -119174,13 +134446,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "vcfannotate", + "bowtie2", + "freebayes", "trimmomatic", + "vcfannotate", "vcffilter2", - "freebayes", "fastqc", - "bowtie2" + "fastq_groomer" ], "update_time": "2022-11-21", "versions": 0 @@ -119203,19 +134475,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ctb_online_data_fetch", - "gmx_makendx", "gmx_solvate", - "add_line_to_file", "param_value_from_file", - "tp_sed_tool", - "gmx_sim", - "compose_text_param", - "tp_text_file_with_recurring_lines", "biomd_neqgamma", + "compose_text_param", + "ctb_online_data_fetch", + "tp_cat", "split_file_to_collection", + "tp_sed_tool", "gmx_em", - "tp_cat" + "tp_text_file_with_recurring_lines", + "gmx_makendx", + "add_line_to_file", + "gmx_sim" ], "update_time": "2022-11-10", "versions": 1 @@ -119225,13 +134497,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", - "Scaffolding", + "k-mer counting", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", "Phasing", - "k-mer counting" + "Scaffolding" ], "edam_topic": [], "id": "4029a0c8fa23d375", @@ -119244,9 +134516,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "quast", + "merqury", "meryl", - "merqury" + "quast" ], "update_time": "2022-11-05", "versions": 1 @@ -119256,20 +134528,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Mapping assembly", - "De-novo assembly", + "Genome assembly", + "Analysis", + "Sequence assembly visualisation", "Sequence assembly", - "Read mapping", - "Read alignment", + "Mapping assembly", + "Scatter plot plotting", "Sequence alignment", + "Cross-assembly", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Analysis", - "Genome assembly", - "Genome indexing", + "De-novo assembly", "Generation", - "Cross-assembly" + "Genome indexing", + "Read alignment", + "Read mapping" ], "edam_topic": [], "id": "bff206b4625375bc", @@ -119282,13 +134554,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "pilon", + "bandage_info", "flye", - "bandage_image", - "nanoplot", "fasta-stats", - "pilon", - "bandage_info" + "nanoplot", + "bandage_image", + "bwa_mem" ], "update_time": "2022-11-03", "versions": 1 @@ -119300,15 +134572,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "f3c8093c5b8a7233", @@ -119323,18 +134595,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2022-11-03", "versions": 1 @@ -119344,9 +134616,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Primer removal", "Read pre-processing", + "Read mapping", "Sequence trimming" ], "edam_topic": [], @@ -119390,11 +134662,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -119408,9 +134680,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "cutadapt", "fastqe", - "cutadapt" + "fastqc" ], "update_time": "2022-10-27", "versions": 1 @@ -119422,15 +134694,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7832cfdeabe47696", @@ -119445,13 +134717,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-10-27", "versions": 1 @@ -119463,19 +134735,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "afd7633a34d68704", @@ -119490,23 +134762,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-10-27", "versions": 1 @@ -119534,17 +134806,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-10-27", "versions": 1 @@ -119593,20 +134865,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-10-20", "versions": 1 @@ -119618,10 +134890,10 @@ ], "doi": "", "edam_operation": [ - "Phylogenetic tree reconstruction", - "Phylogenetic tree analysis", "Pairwise sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "0596162a499b4074", @@ -119640,19 +134912,19 @@ "phylogeny" ], "tools": [ - "ncbi_acc_download", - "collapse_dataset", "bcftools_consensus", + "snpEff", + "__MERGE_COLLECTION__", "snpSift_extractFields", + "collapse_dataset", "rapidnj", - "snpEff_build_gb", - "__MERGE_COLLECTION__", - "snpEff", + "Remove beginning1", + "newick_display", + "ncbi_acc_download", "minimap2", "datamash_ops", - "Remove beginning1", - "lofreq_call", - "newick_display" + "snpEff_build_gb", + "lofreq_call" ], "update_time": "2022-10-18", "versions": 1 @@ -119695,8 +134967,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_plot_heatmap", - "deeptools_compute_matrix" + "deeptools_compute_matrix", + "deeptools_plot_heatmap" ], "update_time": "2022-10-06", "versions": 4 @@ -119706,11 +134978,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", - "Generation", "Pairwise sequence alignment", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "e4d260d46b516b4f", @@ -119723,9 +134995,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "minimap2", - "bwa_mem", - "bowtie2" + "bwa_mem" ], "update_time": "2022-09-30", "versions": 6 @@ -119735,11 +135007,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", - "Generation", "Pairwise sequence alignment", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "8ec186ed3f0470e2", @@ -119752,10 +135024,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "minimap2", - "bwa_mem", "bowtie2", - "hisat2" + "minimap2", + "hisat2", + "bwa_mem" ], "update_time": "2022-09-30", "versions": 7 @@ -119767,13 +135039,13 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Generation", "Genome indexing", - "Sequencing quality control", "Sequence alignment", - "Generation" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "2cbcfeb772f348c9", @@ -119793,9 +135065,9 @@ ], "tools": [ "fastqc", + "ncbi_acc_download", "bwa_mem", - "fastq_groomer", - "ncbi_acc_download" + "fastq_groomer" ], "update_time": "2022-09-30", "versions": 3 @@ -119816,8 +135088,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sort1", "tp_head_tool", + "sort1", "Add_a_column1", "tp_cut_tool" ], @@ -119842,12 +135114,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "spring_model_all", - "__FILTER_FAILED_DATASETS__", - "hhsearch", "collection_element_identifiers", "rbc_splitfasta", + "__FILTER_FAILED_DATASETS__", + "hhsearch", "ffindex_dbkit_merge", + "spring_model_all", "ffindex_dbkit_create", "spring_minz" ], @@ -119859,11 +135131,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", - "Generation", "Pairwise sequence alignment", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "8e9a94fe8e3fef9d", @@ -119876,10 +135148,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "minimap2", - "bwa_mem", "bowtie2", - "hisat2" + "minimap2", + "hisat2", + "bwa_mem" ], "update_time": "2022-09-23", "versions": 2 @@ -119889,11 +135161,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", - "Generation", "Pairwise sequence alignment", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "6d925811544f594b", @@ -119906,10 +135178,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "minimap2", - "bwa_mem", "bowtie2", - "hisat2" + "minimap2", + "hisat2", + "bwa_mem" ], "update_time": "2022-09-22", "versions": 2 @@ -119919,11 +135191,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", - "Generation", "Pairwise sequence alignment", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "2135b0255284752c", @@ -119936,10 +135208,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "minimap2", - "bwa_mem", "bowtie2", - "hisat2" + "minimap2", + "hisat2", + "bwa_mem" ], "update_time": "2022-09-22", "versions": 2 @@ -119949,16 +135221,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "a37961bf3d435918", @@ -119971,16 +135243,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "naive_variant_caller", - "bamleftalign", - "picard_MarkDuplicates", - "trimmomatic", "samtools_mpileup", - "varscan", + "samtools_idxstats", + "trimmomatic", "multiqc", + "varscan", + "bwa_mem", "fastqc", - "samtools_idxstats" + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2022-09-15", "versions": 14 @@ -120009,8 +135281,8 @@ ], "tools": [ "cshl_fastq_quality_filter", - "trimmer", - "cutadapt" + "cutadapt", + "trimmer" ], "update_time": "2022-09-12", "versions": 3 @@ -120031,15 +135303,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_join", + "cshl_fastq_quality_filter", "cat1", - "cshl_fastx_reverse_complement", - "tab2fasta", - "cshl_fastx_renamer", "fastq_to_tabular", - "cshl_fastq_quality_filter", "sort1", - "Grep1" + "cshl_fastx_renamer", + "tab2fasta", + "fastq_join", + "Grep1", + "cshl_fastx_reverse_complement" ], "update_time": "2022-09-09", "versions": 5 @@ -120062,11 +135334,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-08-21", "versions": 0 @@ -120087,20 +135359,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "regexColumn1", "cat1", - "tp_split_on_column", + "datamash_ops", "Add_a_column1", + "Filter1", + "Show beginning1", "tp_sort_header_tool", - "regexColumn1", + "Remove beginning1", "Count1", - "Cut1", + "tabular_to_csv", "join1", "tp_sorted_uniq", - "datamash_ops", - "Remove beginning1", - "tabular_to_csv", - "Show beginning1", - "Filter1" + "Cut1", + "tp_split_on_column" ], "update_time": "2022-08-21", "versions": 2 @@ -120110,8 +135382,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "e067c4e66f0af362", @@ -120124,17 +135396,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "table_compute", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_dada", + "dada2_removeBimeraDenovo", "__FILTER_FAILED_DATASETS__", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", - "dada2_learnErrors", + "table_compute", "__SORTLIST__", - "dada2_dada", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "dada2_learnErrors", + "dada2_mergePairs", + "__UNZIP_COLLECTION__" ], "update_time": "2022-08-02", "versions": 3 @@ -120144,10 +135416,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Sequencing quality control", - "Statistical calculation", - "Sequence composition calculation" + "Sequence composition calculation", + "Read mapping", + "Statistical calculation" ], "edam_topic": [], "id": "2b0d73370a1577b4", @@ -120160,8 +135432,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "bowtie2" + "bowtie2", + "fastqc" ], "update_time": "2022-07-24", "versions": 1 @@ -120171,12 +135443,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "RNA-Seq analysis", - "Genome indexing", "Generation", + "Genome indexing", "Sequence alignment", - "Transcriptome assembly" + "Transcriptome assembly", + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ef2c1fb7d6a51b3a", @@ -120189,11 +135461,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "bowtie2", "bwa", - "hisat2", - "stringtie" + "bwa_mem", + "stringtie", + "hisat2" ], "update_time": "2022-07-13", "versions": 0 @@ -120203,13 +135475,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "d7a11a4dfda3dab4", @@ -120224,8 +135496,8 @@ "metagenomics" ], "tools": [ - "mothur_summary_seqs", "mothur_count_seqs", + "mothur_summary_seqs", "mothur_unique_seqs", "mothur_screen_seqs" ], @@ -120237,16 +135509,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "d653eaefcf6b4697", @@ -120259,39 +135531,39 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_cluster", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_seq_error", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", "mothur_remove_groups", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", + "mothur_pre_cluster", "mothur_get_groups", - "mothur_align_seqs", + "mothur_chimera_vsearch", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_cluster", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", - "XY_Plot_1", - "mothur_seq_error" + "XY_Plot_1" ], "update_time": "2022-07-03", "versions": 0 @@ -120301,16 +135573,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "775335812a6b7a61", @@ -120323,39 +135595,39 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_cluster", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_seq_error", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", "mothur_remove_groups", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", + "mothur_pre_cluster", "mothur_get_groups", - "mothur_align_seqs", + "mothur_chimera_vsearch", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_cluster", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", - "XY_Plot_1", - "mothur_seq_error" + "XY_Plot_1" ], "update_time": "2022-07-03", "versions": 0 @@ -120378,15 +135650,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2022-06-30", "versions": 1 @@ -120409,15 +135681,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ambertools_acpype", - "Cut1", + "ambertools_antechamber", + "gmx_setup", "param_value_from_file", - "tp_grep_tool", "gmx_merge_topology_files", - "openbabel_compound_convert", - "ambertools_antechamber", "ctb_rdkit_descriptors", - "gmx_setup" + "Cut1", + "ambertools_acpype", + "openbabel_compound_convert", + "tp_grep_tool" ], "update_time": "2022-06-30", "versions": 1 @@ -120440,21 +135712,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2022-06-30", "versions": 1 @@ -120477,21 +135749,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gmx_editconf", - "md_converter", - "collapse_dataset", - "Cut1", "gmx_solvate", - "parmconv", "param_value_from_file", - "tp_grep_tool", - "mmpbsa_mmgbsa", - "gmx_sim", - "Summary_Statistics1", + "collapse_dataset", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", "split_file_to_collection", - "gmx_em" + "Summary_Statistics1", + "gmx_em", + "tp_text_file_with_recurring_lines", + "parmconv", + "mmpbsa_mmgbsa", + "gmx_editconf", + "tp_grep_tool", + "md_converter", + "gmx_sim" ], "update_time": "2022-06-30", "versions": 1 @@ -120501,12 +135773,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Variant calling", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "0ee0493f3168cbb3", @@ -120519,14 +135791,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "naive_variant_caller", - "varscan_mpileup", "samtools_mpileup", "freebayes", "multiqc", - "fastqc", - "bowtie2", - "ivar_variants" + "ivar_variants", + "varscan_mpileup", + "fastqc" ], "update_time": "2022-06-21", "versions": 16 @@ -120536,12 +135808,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "RNA-Seq quantification" + "Read mapping" ], "edam_topic": [], "id": "73d98e5f821a78b3", @@ -120554,12 +135826,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "bowtie2", "fastq_quality_trimmer", "featurecounts", + "tp_cat", "fastqc", - "bowtie2", - "tp_cat" + "fastq_groomer" ], "update_time": "2022-06-21", "versions": 8 @@ -120569,9 +135841,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Peak calling", "Read mapping", "Enrichment analysis", - "Peak calling", "Gene regulatory network analysis" ], "edam_topic": [], @@ -120587,10 +135859,10 @@ "chipseq" ], "tools": [ - "wig_to_bigWig", + "bowtie2", "macs2_callpeak", - "fastq_groomer", - "bowtie2" + "wig_to_bigWig", + "fastq_groomer" ], "update_time": "2022-06-16", "versions": 4 @@ -120614,8 +135886,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2022-06-16", "versions": 1 @@ -120627,10 +135899,10 @@ ], "doi": "", "edam_operation": [ - "Phylogenetic tree reconstruction", - "Phylogenetic tree analysis", "Pairwise sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree analysis", + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "005924662f68a480", @@ -120649,19 +135921,19 @@ "phylogeny" ], "tools": [ - "ncbi_acc_download", - "collapse_dataset", "bcftools_consensus", + "snpEff", + "__MERGE_COLLECTION__", "snpSift_extractFields", + "collapse_dataset", "rapidnj", - "snpEff_build_gb", - "__MERGE_COLLECTION__", - "snpEff", + "Remove beginning1", + "newick_display", + "ncbi_acc_download", "minimap2", "datamash_ops", - "Remove beginning1", - "lofreq_call", - "newick_display" + "snpEff_build_gb", + "lofreq_call" ], "update_time": "2022-06-14", "versions": 14 @@ -120671,14 +135943,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Sequence composition calculation", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", - "Sequence alignment" + "Genome indexing", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "8c4fcd4bd9d5a72d", @@ -120691,15 +135963,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bcftools_call", "vcffilter2", "bcftools_plugin_counts", - "bwa", - "bcftools_call", + "bedtools_intersectbed", "gtftobed12", + "Grep1", "fastqc", "bcftools_mpileup", - "Grep1", - "bedtools_intersectbed" + "bwa" ], "update_time": "2022-06-09", "versions": 13 @@ -120709,14 +135981,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Gene expression analysis", + "Sequence alignment", + "Sequencing quality control", + "Transcriptome assembly", + "Sequence composition calculation", "RNA-Seq quantification", - "Statistical calculation", - "RNA-Seq analysis", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "b1b75a9323d25085", @@ -120729,15 +136001,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "samtools_sort", "deeptools_bam_coverage", - "rna_star", - "fastq_paired_end_deinterlacer", "salmon", - "umi_tools_count", - "samtools_sort", + "qualimap_rnaseq", + "fastq_paired_end_deinterlacer", "fastqc", + "rna_star", "stringtie", - "qualimap_rnaseq" + "umi_tools_count" ], "update_time": "2022-06-07", "versions": 25 @@ -120765,18 +136037,18 @@ "generic" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-06-03", "versions": 3 @@ -120786,13 +136058,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "4b7e73bb7ac93c95", @@ -120805,15 +136077,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "mothur_fastq_info", + "fastq_quality_trimmer", + "fastq_to_fasta_python", "fastq_join", - "fasta_merge_files_and_filter_unique_sequences", + "cat_multiple", "filter_by_fasta_ids", + "fasta_merge_files_and_filter_unique_sequences", "cshl_fastx_reverse_complement", - "fastq_quality_trimmer", - "mothur_unique_seqs", - "cat_multiple", - "mothur_fastq_info", - "fastq_to_fasta_python" + "mothur_unique_seqs" ], "update_time": "2022-06-02", "versions": 14 @@ -120825,18 +136097,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "0fa2ce12c2874b1d", @@ -120853,21 +136125,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-06-02", "versions": 1 @@ -120879,18 +136151,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "d96bd5c9fb553f2c", @@ -120907,21 +136179,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-06-02", "versions": 1 @@ -120933,18 +136205,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "4b41a8247f52c463", @@ -120961,21 +136233,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-06-02", "versions": 1 @@ -121001,18 +136273,18 @@ "generic" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2022-06-01", "versions": 3 @@ -121024,14 +136296,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "33ae58f05e5e1d60", @@ -121047,18 +136319,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-05-31", "versions": 6 @@ -121068,13 +136340,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Primer removal", "Read pre-processing", - "Sequence trimming", - "RNA-Seq analysis", "Sequence alignment", - "Transcriptome assembly" + "Transcriptome assembly", + "Primer removal", + "Sequence trimming", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "73ef57dfa532af3d", @@ -121093,8 +136365,8 @@ "tools": [ "stringtie", "hisat2", - "trim_galore", - "fastq_dump" + "fastq_dump", + "trim_galore" ], "update_time": "2022-05-30", "versions": 1 @@ -121104,15 +136376,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "De-novo assembly", - "Sequencing quality control", "Gene prediction", "Genome annotation", "Genome assembly", - "Coding region prediction", "Mapping assembly", - "Cross-assembly" + "Sequencing quality control", + "Cross-assembly", + "Coding region prediction", + "De-novo assembly", + "Filtering" ], "edam_topic": [], "id": "7fc8b2398b6f093f", @@ -121126,10 +136398,10 @@ "tags": [], "tools": [ "jcvi_gff_stats", - "flye", - "filtlong", "prokka", - "ncbi_blastn_wrapper" + "flye", + "ncbi_blastn_wrapper", + "filtlong" ], "update_time": "2022-05-28", "versions": 12 @@ -121154,9 +136426,9 @@ "tags": [], "tools": [ "rna_star", + "trimmomatic", "htseq_count", - "fastq_groomer", - "trimmomatic" + "fastq_groomer" ], "update_time": "2022-05-24", "versions": 0 @@ -121166,13 +136438,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -121186,11 +136458,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2022-05-23", @@ -121201,11 +136473,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -121219,8 +136491,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2022-05-23", "versions": 0 @@ -121230,13 +136502,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -121250,11 +136522,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2022-05-22", @@ -121265,13 +136537,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -121285,11 +136557,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2022-05-21", @@ -121313,11 +136585,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-20", "versions": 0 @@ -121340,11 +136612,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-20", "versions": 1 @@ -121354,13 +136626,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -121374,11 +136646,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2022-05-20", @@ -121403,8 +136675,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_stats", "bowtie2", + "samtools_stats", "jbrowse" ], "update_time": "2022-05-20", @@ -121415,11 +136687,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -121433,8 +136705,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2022-05-20", "versions": 0 @@ -121457,11 +136729,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-20", "versions": 3 @@ -121471,11 +136743,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -121489,8 +136761,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "cutadapt" + "cutadapt", + "fastqc" ], "update_time": "2022-05-18", "versions": 0 @@ -121513,11 +136785,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-14", "versions": 1 @@ -121540,11 +136812,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-13", "versions": 0 @@ -121567,11 +136839,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-05-13", "versions": 0 @@ -121624,15 +136896,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Differential gene expression analysis", "Sequencing quality control", + "Sequence composition calculation", + "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Read mapping", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "5a272f266a1fa4ac", @@ -121645,11 +136917,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "featurecounts", - "fastq_dump", "fastqc", - "deseq2", - "bowtie2" + "fastq_dump", + "deseq2" ], "update_time": "2022-05-03", "versions": 1 @@ -121659,17 +136931,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree analysis", - "Sequence read processing", - "Sequencing quality control", - "Phylogenetic analysis", - "Phylogenetic tree generation", - "DNA barcoding", "Visualisation", - "Phylogenetic tree reconstruction", "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic tree analysis", + "Phylogenetic analysis", "Multiple sequence alignment", + "Phylogenetic tree reconstruction", "Sequence analysis", + "Sequence read processing", "Taxonomic classification" ], "edam_topic": [], @@ -121688,10 +136960,10 @@ ], "tools": [ "rbc_mafft", - "iqtree", - "newick_display", "mothur_fastq_info", - "clustalw" + "newick_display", + "clustalw", + "iqtree" ], "update_time": "2022-04-26", "versions": 3 @@ -121718,13 +136990,13 @@ "scatterplot" ], "tools": [ - "ggplot2_point", - "tp_cut_tool", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "tp_cut_tool", + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-04-25", "versions": 12 @@ -121734,8 +137006,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -121749,13 +137021,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", - "samtools_flagstat", - "samtools_sort", + "bowtie2", "freebayes", - "bcftools_stats", + "samtools_sort", + "deeptools_bam_coverage", "bcftools_filter", - "bowtie2" + "bcftools_stats", + "samtools_flagstat" ], "update_time": "2022-04-18", "versions": 6 @@ -121765,8 +137037,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -121780,13 +137052,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", - "samtools_flagstat", - "samtools_sort", + "bowtie2", "freebayes", - "bcftools_stats", + "samtools_sort", + "deeptools_bam_coverage", "bcftools_filter", - "bowtie2" + "bcftools_stats", + "samtools_flagstat" ], "update_time": "2022-04-18", "versions": 9 @@ -121797,9 +137069,9 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", "Phylogenetic tree generation", - "Genome visualisation" + "Genome visualisation", + "Variant calling" ], "edam_topic": [], "id": "ee4679b3e9e830b7", @@ -121823,10 +137095,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Sequencing quality control", - "Statistical calculation", - "Sequence composition calculation" + "Sequence composition calculation", + "Read mapping", + "Statistical calculation" ], "edam_topic": [], "id": "3dbe754882a263cd", @@ -121839,11 +137111,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "jvarkit_wgscoverageplotter", - "varscan_mpileup", + "bowtie2", "samtools_mpileup", - "fastqc", - "bowtie2" + "varscan_mpileup", + "jvarkit_wgscoverageplotter", + "fastqc" ], "update_time": "2022-04-06", "versions": 40 @@ -121875,10 +137147,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Sequence alignment", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "02ff4efb583aaf49", @@ -121891,10 +137163,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa", - "bwa_mem", "bowtie2", - "hisat2" + "hisat2", + "bwa_mem", + "bwa" ], "update_time": "2022-04-04", "versions": 3 @@ -121915,8 +137187,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "cat_multiple" ], "update_time": "2022-04-02", @@ -121938,8 +137210,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "cat_multiple" ], "update_time": "2022-04-02", @@ -121963,13 +137235,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-04-02", "versions": 2 @@ -121981,14 +137253,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "7dde0721a382ea3e", @@ -122005,26 +137277,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2022-03-31", "versions": 1 @@ -122034,10 +137306,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Sequence alignment", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment", + "Read mapping" ], "edam_topic": [], "id": "303af6cec326947c", @@ -122050,10 +137322,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa", - "bwa_mem", "bowtie2", - "hisat2" + "hisat2", + "bwa", + "bwa_mem" ], "update_time": "2022-03-22", "versions": 2 @@ -122084,17 +137356,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Gene expression analysis", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "dec0cf06fa059e65", @@ -122107,20 +137379,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "tp_cut_tool", + "Filter1", + "gprofiler_gost", + "tp_head_tool", + "tp_tail_tool", + "salmon", + "fasterq_dump", "tp_awk_tool", "trim_galore", - "fasterq_dump", - "salmon", "Convert characters1", - "hgv_david", "fastqc", - "tp_head_tool", - "Filter1", - "deseq2", - "tp_tail_tool" + "tp_cut_tool", + "hgv_david", + "deseq2" ], "update_time": "2022-03-21", "versions": 9 @@ -122130,17 +137402,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Gene expression analysis", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "092be3cf6e40282c", @@ -122153,19 +137425,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "tp_cut_tool", + "Filter1", + "gprofiler_gost", + "tp_head_tool", + "tp_tail_tool", + "salmon", + "fasterq_dump", "tp_awk_tool", "trim_galore", - "fasterq_dump", - "salmon", - "hgv_david", "fastqc", - "tp_head_tool", - "Filter1", - "deseq2", - "tp_tail_tool" + "tp_cut_tool", + "hgv_david", + "deseq2" ], "update_time": "2022-03-21", "versions": 8 @@ -122175,16 +137447,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "43c39bc86399188f", @@ -122198,20 +137470,20 @@ "tags": [], "tools": [ "limma_voom", - "table_compute", - "tp_cut_tool", - "trim_galore", - "fasterq_dump", + "Filter1", + "filter_tabular", + "tp_tail_tool", "salmon", + "fasterq_dump", "tp_replace_in_line", - "filter_tabular", + "trim_galore", + "table_compute", "tp_sed_tool", - "hgv_david", - "csv_to_tabular", "collection_column_join", + "csv_to_tabular", "fastqc", - "Filter1", - "tp_tail_tool" + "tp_cut_tool", + "hgv_david" ], "update_time": "2022-03-21", "versions": 0 @@ -122221,16 +137493,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "5203bc68df3cf819", @@ -122243,18 +137515,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_multijoin_tool", "limma_voom", - "tp_cut_tool", - "trim_galore", - "fasterq_dump", + "Filter1", + "tp_head_tool", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "tp_multijoin_tool", "tp_sed_tool", - "hgv_david", "fastqc", - "tp_head_tool", - "Filter1", - "tp_tail_tool" + "tp_cut_tool", + "hgv_david" ], "update_time": "2022-03-20", "versions": 3 @@ -122264,8 +137536,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Data handling" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0c052e50594f6d2d", @@ -122279,13 +137551,13 @@ "tags": [], "tools": [ "limma_voom", - "tp_cut_tool", + "Filter1", + "tp_head_tool", + "tp_tail_tool", "fasterq_dump", "tp_sed_tool", - "hgv_david", - "tp_head_tool", - "Filter1", - "tp_tail_tool" + "tp_cut_tool", + "hgv_david" ], "update_time": "2022-03-20", "versions": 0 @@ -122295,15 +137567,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Formatting", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Formatting", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "feeec17310351914", @@ -122316,14 +137588,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "vcffilter2", "freebayes", + "picard_CleanSam", "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "bwa_mem", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2022-03-19", "versions": 0 @@ -122349,20 +137621,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -122388,20 +137660,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -122427,20 +137699,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -122466,20 +137738,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -122505,20 +137777,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -122546,8 +137818,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -122575,8 +137847,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -122604,8 +137876,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -122618,11 +137890,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "db01ac5b0dc50cd4", @@ -122638,15 +137910,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122659,11 +137931,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "53dda64a5a6ebd54", @@ -122679,15 +137951,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122699,15 +137971,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "10c2136973c88d8a", @@ -122723,17 +137995,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122745,15 +138017,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "26b35874b9e32355", @@ -122771,17 +138043,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122793,15 +138065,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "5b3e2ddf525da25d", @@ -122819,17 +138091,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122841,15 +138113,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bbe6f5a45ea5ee5e", @@ -122867,17 +138139,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -122889,14 +138161,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "6b11d738ee57f245", @@ -122913,22 +138185,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -122940,14 +138212,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bd355e8ce58a139e", @@ -122964,22 +138236,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -122991,14 +138263,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "e282f505ba9f729f", @@ -123015,22 +138287,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123042,14 +138314,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bf3ccae8d5b6ef58", @@ -123066,22 +138338,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123093,14 +138365,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "4cf8cc42e97b2da6", @@ -123117,22 +138389,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123144,14 +138416,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "98b2ac8fc75781f8", @@ -123168,22 +138440,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123195,15 +138467,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "d3428dd172a78102", @@ -123221,20 +138493,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123246,15 +138518,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "c12e6b7896f8e114", @@ -123272,20 +138544,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123297,15 +138569,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "9adf8691809326e5", @@ -123323,20 +138595,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -123348,16 +138620,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "4357180d40560019", @@ -123375,27 +138647,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -123407,16 +138679,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "c7b2d2ccc4b0dec5", @@ -123434,27 +138706,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -123482,18 +138754,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -123521,18 +138793,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -123560,18 +138832,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -123599,18 +138871,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -123633,11 +138905,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 0 @@ -123647,13 +138919,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "00a501a1fada4104", @@ -123668,9 +138940,9 @@ "tools": [ "featurecounts", "multiqc", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2" ], "update_time": "2022-03-15", "versions": 0 @@ -123680,12 +138952,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Formatting", - "Variant calling" + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "bf90f2bd20fbff21", @@ -123698,15 +138970,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "varscan_mpileup", - "trimmomatic", + "bowtie2", "samtools_mpileup", "samtools_rmdup", "freebayes", + "trimmomatic", + "ivar_variants", + "varscan_mpileup", "picard_SortSam", - "fastqc", - "bowtie2", - "ivar_variants" + "fastqc" ], "update_time": "2022-03-15", "versions": 20 @@ -123727,8 +138999,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "cat_multiple" ], "update_time": "2022-03-14", @@ -123750,9 +139022,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gops_intersect_1", "Filter1", - "gops_concat_1", - "gops_intersect_1" + "gops_concat_1" ], "update_time": "2022-03-14", "versions": 1 @@ -123762,14 +139034,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Data handling", + "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "Sequence composition calculation", - "Sequence annotation", "Sequencing quality control", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence annotation" ], "edam_topic": [], "id": "4e6005819e57ed35", @@ -123782,12 +139054,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "gffread", - "fastq_dump", "featurecounts", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-03-11", "versions": 1 @@ -123797,14 +139069,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Data handling", + "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "Sequence composition calculation", - "Sequence annotation", "Sequencing quality control", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence annotation" ], "edam_topic": [], "id": "7b19452fe35b8b17", @@ -123817,12 +139089,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "gffread", - "fastq_dump", "featurecounts", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2022-03-11", "versions": 5 @@ -123833,10 +139105,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "3c7349268d74c576", @@ -123849,11 +139121,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "seq_filter_by_id", + "EMBOSS: transeq101", "fasta2tab", + "tp_sed_tool", "filter_by_fasta_ids", - "EMBOSS: transeq101", - "tp_sed_tool" + "seq_filter_by_id" ], "update_time": "2022-03-09", "versions": 2 @@ -123863,16 +139135,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", + "Sequence contamination filtering", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Sequence contamination filtering", "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "1f48b44fa22ac5fc", @@ -123885,14 +139157,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "lofreq_viterbi", - "fastp", "ngsutils_bam_filter", + "lofreq_viterbi", "ivar_consensus", - "qualimap_bamqc", - "ivar_variants" + "fastp", + "ivar_variants", + "bwa_mem", + "bamleftalign", + "qualimap_bamqc" ], "update_time": "2022-03-07", "versions": 10 @@ -123902,8 +139174,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "806ef8816168916f", @@ -123916,14 +139188,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", "dada2_learnErrors", - "dada2_dada", - "dada2_removeBimeraDenovo" + "dada2_mergePairs" ], "update_time": "2022-02-24", "versions": 0 @@ -123946,11 +139218,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-02-20", "versions": 3 @@ -123976,20 +139248,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-01-31", "versions": 0 @@ -123999,13 +139271,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence assembly validation", + "Sequence composition calculation", "Visualisation", "Statistical calculation", - "Sequence composition calculation", "Genome assembly", - "Sequencing quality control" + "Sequence assembly validation", + "Sequencing quality control", + "Aggregation" ], "edam_topic": [], "id": "a67afbea4b2eb26b", @@ -124018,11 +139290,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "unicycler", "trimmomatic", - "quast", - "fastqc", "ncbi_blastn_wrapper", - "unicycler" + "quast", + "fastqc" ], "update_time": "2022-01-28", "versions": 2 @@ -124032,16 +139304,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e2d7b8a4e6c422a3", @@ -124055,20 +139327,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "vcffilter2", + "samtools_idxstats", + "sort1", "table_annovar", + "vcffilter2", + "bam_to_sam", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-26", "versions": 0 @@ -124078,16 +139350,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "3bed12ef73ba93bf", @@ -124101,23 +139373,23 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", "snpEff_download", - "vcffilter2", - "Summary_Statistics1", - "table_annovar", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "vcffilter2", + "snpEff", + "bam_to_sam", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-26", "versions": 0 @@ -124127,11 +139399,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping" ], "edam_topic": [], "id": "839cac17365affb7", @@ -124148,10 +139420,10 @@ "bioinformatics" ], "tools": [ - "fastqc", "bowtie2", + "trimmomatic", "multiqc", - "trimmomatic" + "fastqc" ], "update_time": "2022-01-26", "versions": 6 @@ -124161,8 +139433,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Genome visualisation", + "Read mapping", "Nucleic acid sequence analysis", "Differential gene expression analysis" ], @@ -124177,12 +139449,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "htseq_count", + "bowtie2", "edger", "trimmomatic", - "htseq_count", "tabular_to_csv", - "jbrowse", - "bowtie2" + "jbrowse" ], "update_time": "2022-01-26", "versions": 0 @@ -124192,18 +139464,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Sequence trimming", "Sequence contamination filtering", + "Sequence alignment", "Primer removal", - "Read pre-processing", + "Sequencing quality control", "Sequence file editing", + "Formatting", + "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "35c2626849348f2c", @@ -124216,15 +139488,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cd_hit_dup", - "picard_MarkDuplicates", "samtools_fastx", - "bwa", - "samtools_view", - "fastp", "cutadapt", + "fastp", + "bam_to_sam", + "cd_hit_dup", "seqtk_mergepe", - "bam_to_sam" + "bwa", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-01-25", "versions": 47 @@ -124234,14 +139506,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "9b4323b68f609e06", @@ -124257,15 +139529,15 @@ ], "tools": [ "cat1", - "bwa_mem", - "fastq_groomer", - "vcffilter2", - "table_annovar", - "freebayes", + "vcfselectsamples", "sort1", + "freebayes", + "table_annovar", + "vcffilter2", "Grouping1", + "bwa_mem", "fastqc", - "vcfselectsamples" + "fastq_groomer" ], "update_time": "2022-01-19", "versions": 1 @@ -124275,17 +139547,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ddb737f2ad0589e8", @@ -124298,23 +139570,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "tp_cut_tool", - "Cut1", + "Filter1", "gffread", - "trim_galore", - "join1", - "fasterq_dump", + "gprofiler_gost", + "tp_find_and_replace", + "tp_tail_tool", "salmon", + "fasterq_dump", "melt", - "tp_find_and_replace", + "trim_galore", + "column_order_header_sort", "collection_column_join", - "__RELABEL_FROM_FILE__", + "join1", "fastqc", - "column_order_header_sort", - "Filter1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2022-01-18", "versions": 2 @@ -124324,15 +139596,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "76b8ed1c68678b62", @@ -124345,11 +139617,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rna_star", - "rseqc_infer_experiment", + "cutadapt", "multiqc", "fastqc", - "cutadapt" + "rna_star", + "rseqc_infer_experiment" ], "update_time": "2022-01-16", "versions": 2 @@ -124359,16 +139631,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "22f6b939e97d3b47", @@ -124382,21 +139654,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-12", "versions": 0 @@ -124406,16 +139678,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d85f8ef78040fbb1", @@ -124429,22 +139701,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "vcffilter2", + "samtools_idxstats", + "sort1", "table_annovar", - "Summary_Statistics1", "snpEff", - "freebayes", - "samtool_filter2", - "sort1", - "fastqc", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-10", "versions": 0 @@ -124454,16 +139726,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "bb16936081b820f6", @@ -124476,28 +139748,28 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", "snpSift_extractFields", - "lofreq_call", + "trimmomatic", + "picard_AddOrReplaceReadGroups", "fastqc", - "samtools_idxstats", - "vcf2tsv", + "lofreq_call", "vcfsort", - "bam_to_sam", - "vcffilter2", - "table_annovar", - "freebayes", "sort1", - "snpEff", + "Filter1", + "samtools_idxstats", + "table_annovar", + "vcffilter2", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", - "Summary_Statistics1", - "samtool_filter2", - "Filter1", "bedtools_coveragebed", - "picard_AddOrReplaceReadGroups" + "snpEff", + "bam_to_sam", + "Summary_Statistics1", + "vcf2tsv", + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2022-01-10", "versions": 0 @@ -124507,16 +139779,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "bfee1238c70627cb", @@ -124530,22 +139802,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-10", "versions": 0 @@ -124555,16 +139827,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e6b803c1232cd08e", @@ -124578,21 +139850,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-10", "versions": 0 @@ -124602,16 +139874,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ec96e3bf30d5f771", @@ -124625,21 +139897,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "vcffilter2", + "samtools_idxstats", + "sort1", "table_annovar", + "Filter1", + "vcffilter2", + "bam_to_sam", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-08", "versions": 0 @@ -124649,16 +139921,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "50206b10de958d03", @@ -124671,27 +139943,27 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", "snpSift_extractFields", - "lofreq_call", + "trimmomatic", "fastqc", - "samtools_idxstats", - "vcf2tsv", + "lofreq_call", "vcfsort", - "bam_to_sam", - "vcffilter2", - "table_annovar", - "freebayes", "sort1", - "snpEff", + "Filter1", + "samtools_idxstats", + "table_annovar", + "vcffilter2", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "vcf2tsv", + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2022-01-04", "versions": 0 @@ -124701,16 +139973,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "fae519dcba6bfc72", @@ -124723,27 +139995,27 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", "snpSift_extractFields", - "lofreq_call", + "trimmomatic", "fastqc", - "samtools_idxstats", - "vcf2tsv", + "lofreq_call", "vcfsort", - "bam_to_sam", - "vcffilter2", - "table_annovar", - "freebayes", "sort1", - "snpEff", + "Filter1", + "samtools_idxstats", + "table_annovar", + "vcffilter2", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "vcf2tsv", + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2022-01-04", "versions": 0 @@ -124753,16 +140025,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ab8590a0ee1b9951", @@ -124776,22 +140048,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "snpEff", + "table_annovar", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-03", "versions": 0 @@ -124801,16 +140073,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "0660a00407fc16a1", @@ -124824,22 +140096,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "snpEff", + "table_annovar", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2022-01-03", "versions": 0 @@ -124849,14 +140121,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "dfa8c64634aec75c", @@ -124869,17 +140141,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpEff_download", - "snpSift_extractFields", "snpEff", + "snpSift_extractFields", + "snpEff_download", "lofreq_viterbi", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bcftools_view" + "bcftools_view", + "lofreq_indelqual", + "bwa_mem", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-12-25", "versions": 0 @@ -124907,19 +140179,19 @@ "networkanalysis" ], "tools": [ - "netisce5", + "netisce2", + "netisce4", + "netisce3", "netisce12", - "netisce9", "netisce13", - "netisce7", + "netisce11", + "netisce1", "netisce10", + "netisce9", "netisce6", - "netisce2", - "netisce3", + "netisce7", "netisce8", - "netisce11", - "netisce4", - "netisce1" + "netisce5" ], "update_time": "2021-12-23", "versions": 1 @@ -124929,16 +140201,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "b33ad2032a655706", @@ -124951,29 +140223,29 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", + "snpEff_databases", "fastqc", + "CONVERTER_bam_to_coodinate_sorted_bam", + "sort1", + "Filter1", "samtools_idxstats", - "bam_to_sam", - "vcffilter2", "table_annovar", - "CONVERTER_interval_to_bedstrict_0", - "freebayes", - "sort1", - "bcftools_stats", - "CONVERTER_bam_to_bigwig_0", - "snpEff_databases", - "snpEff_download", - "snpEff", - "CONVERTER_bam_to_coodinate_sorted_bam", + "vcffilter2", "bwa_mem", + "CONVERTER_bam_to_bigwig_0", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "CONVERTER_interval_to_bedstrict_0", + "bcftools_stats", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2021-12-22", "versions": 0 @@ -124994,8 +140266,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "tp_cat" ], "update_time": "2021-12-16", @@ -125007,9 +140279,9 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Primer removal", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -125024,9 +140296,9 @@ "tags": [], "tools": [ "cshl_fastq_quality_filter", - "fastp", "cshl_fastx_reverse_complement", - "cutadapt" + "cutadapt", + "fastp" ], "update_time": "2021-12-13", "versions": 19 @@ -125036,16 +140308,16 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene expression analysis", + "Sequence alignment", + "Transcriptome assembly", "Sequence composition calculation", + "Generation", + "Genome indexing", + "RNA-Seq quantification", "Read mapping", "Gene expression profiling", - "Sequence alignment", - "Gene expression analysis", - "RNA-Seq quantification", - "RNA-Seq analysis", - "Genome indexing", - "Generation", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c2c6779a8b1821e0", @@ -125058,12 +140330,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_paired_end_deinterlacer", - "stringtie", + "bowtie2", "kallisto_quant", "salmon", - "bowtie2" + "fastq_paired_end_deinterlacer", + "bwa_mem", + "stringtie" ], "update_time": "2021-12-08", "versions": 1 @@ -125073,16 +140345,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Gene expression profiling", "Gene expression analysis", "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", - "Genome indexing", + "Sequence composition calculation", "Generation", - "RNA-Seq quantification" + "Genome indexing", + "RNA-Seq quantification", + "Read mapping", + "Gene expression profiling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "08bdcecd1cb0bda3", @@ -125095,10 +140367,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "bowtie2", "kallisto_quant", "salmon", + "bwa_mem", "stringtie" ], "update_time": "2021-12-08", @@ -125109,14 +140381,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", "Statistical calculation", - "RNA-Seq analysis", - "Transcriptome assembly" + "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", + "Transcriptome assembly", + "Sequence composition calculation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "b77fa73d4fbde131", @@ -125130,13 +140402,13 @@ "tags": [], "tools": [ "trimmomatic", - "fastq_dump", "stringtie_merge", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "stringtie" + "stringtie", + "hisat2", + "fastq_dump", + "deseq2" ], "update_time": "2021-12-07", "versions": 0 @@ -125146,17 +140418,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "07fdeadce7a6d5cb", @@ -125169,17 +140441,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "__RELABEL_FROM_FILE__", "limma_voom", - "tp_cut_tool", - "Cut1", "gffread", - "trim_galore", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", "collection_column_join", "fastqc", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2021-12-01", "versions": 4 @@ -125189,19 +140461,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", + "Gene prediction", + "Genome annotation", + "Visualisation", + "Statistical calculation", "Genome assembly", - "Multilocus sequence typing", "Sequence assembly visualisation", + "Multilocus sequence typing", + "Sequencing quality control", + "Coding region prediction", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", "Antimicrobial resistance prediction", - "Gene prediction", - "Genome annotation", - "Taxonomic classification", - "Statistical calculation", - "Coding region prediction" + "Taxonomic classification" ], "edam_topic": [], "id": "fb01e1a49793c8be", @@ -125214,16 +140486,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "abricate", + "prokka", "trimmomatic", - "kraken", "mlst", + "spades", + "abricate", "bandage_image", - "quast", "kraken-report", - "prokka", + "quast", "fastqc", - "spades" + "kraken" ], "update_time": "2021-11-29", "versions": 16 @@ -125246,11 +140518,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2021-11-09", "versions": 1 @@ -125272,8 +140544,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "spring_map", - "collapse_dataset" + "collapse_dataset", + "spring_map" ], "update_time": "2021-11-04", "versions": 1 @@ -125298,13 +140570,13 @@ "name:test" ], "tools": [ - "ggplot2_point", - "Cut1", - "datamash_ops", "sort1", + "Cut1", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2021-11-03", "versions": 6 @@ -125348,8 +140620,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mlst", - "ncbi_acc_download" + "ncbi_acc_download", + "mlst" ], "update_time": "2021-11-01", "versions": 3 @@ -125419,11 +140691,11 @@ "name:suhasini" ], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2021-10-22", "versions": 2 @@ -125448,13 +140720,13 @@ "name:suhasini" ], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2021-10-22", "versions": 3 @@ -125464,17 +140736,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", + "Sequence alignment analysis", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "5641d1cbe795203f", @@ -125487,15 +140759,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bamleftalign", - "picard_MarkDuplicates", + "freebayes", "cshl_fastx_trimmer", + "qualimap_bamqc", "bcftools_plugin_counts", - "bwa", - "freebayes", "fastqc", - "qualimap_bamqc", - "bamFilter" + "bamFilter", + "bwa", + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2021-10-19", "versions": 0 @@ -125505,18 +140777,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "044c5ce43f2e1829", @@ -125529,18 +140801,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_MarkDuplicates", - "rna_star", - "rseqc_read_distribution", - "featurecounts", - "rseqc_infer_experiment", - "gtftobed12", + "rseqc_geneBody_coverage", "sort1", + "samtools_idxstats", + "featurecounts", "multiqc", - "rseqc_geneBody_coverage", + "gtftobed12", "fastqc", - "samtools_idxstats", - "cutadapt" + "rna_star", + "cutadapt", + "rseqc_infer_experiment", + "rseqc_read_distribution", + "picard_MarkDuplicates" ], "update_time": "2021-10-18", "versions": 0 @@ -125561,12 +140833,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "get_flanks1", "CONVERTER_interval_to_bed_0", + "tp_tail_tool", + "gops_intersect_1", "Grouping1", "tp_replace_in_column", - "gops_intersect_1", - "tp_tail_tool" + "get_flanks1" ], "update_time": "2021-10-18", "versions": 0 @@ -125578,16 +140850,16 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Visualisation", "Statistical calculation", - "Taxonomic classification", + "Sequence alignment", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping", + "Taxonomic classification" ], "edam_topic": [], "id": "b68ec42db8953569", @@ -125605,14 +140877,14 @@ "microbiome" ], "tools": [ - "Kraken2Tax", - "trimmomatic", "kraken2", + "trimmomatic", + "picard_SamToFastq", + "taxonomy_krona_chart", + "fastqc", "bwa", "samtools_view", - "taxonomy_krona_chart", - "picard_SamToFastq", - "fastqc" + "Kraken2Tax" ], "update_time": "2021-10-18", "versions": 0 @@ -125635,11 +140907,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "tp_head_tool", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2021-10-16", "versions": 1 @@ -125662,13 +140934,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ggplot2_point", - "tp_cut_tool", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "tp_cut_tool", + "ggplot2_point", + "datamash_ops" ], "update_time": "2021-10-11", "versions": 0 @@ -125693,11 +140965,11 @@ "genome" ], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2021-10-09", "versions": 2 @@ -125707,17 +140979,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "6cb8b40b819f2764", @@ -125730,15 +141002,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", + "picard_CleanSam", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "freebayes", + "picard_AddOrReplaceReadGroups", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2021-09-30", "versions": 0 @@ -125761,12 +141033,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_norm", - "Add_a_column1", + "bowtie2", "param_value_from_file", - "datamash_ops", + "Add_a_column1", + "bcftools_norm", "compose_text_param", - "bowtie2" + "datamash_ops" ], "update_time": "2021-09-30", "versions": 2 @@ -125788,8 +141060,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "spring_map", - "collapse_dataset" + "collapse_dataset", + "spring_map" ], "update_time": "2021-09-29", "versions": 2 @@ -125821,15 +141093,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "e035be74e3c85bf5", @@ -125842,11 +141114,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cutadapt", + "multiqc", "fastqc", "rna_star", - "rseqc_infer_experiment", - "multiqc", - "cutadapt" + "rseqc_infer_experiment" ], "update_time": "2021-09-25", "versions": 0 @@ -125856,11 +141128,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "6be2c7930c391b35", @@ -125878,15 +141150,15 @@ "draft" ], "tools": [ - "bwa_mem", - "bedtools_bamtobed", "bcftools_consensus", + "snpEff", "snpSift_extractFields", + "bedtools_mergebed", + "bedtools_bamtobed", + "bwa_mem", "snpEff_build_gb", - "snpEff", - "bedtools_getfastabed", "lofreq_call", - "bedtools_mergebed" + "bedtools_getfastabed" ], "update_time": "2021-09-24", "versions": 7 @@ -125896,12 +141168,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", - "Sequencing quality control", + "Statistical calculation", + "Transcriptome assembly", "Sequence alignment", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "35209d092e636cd8", @@ -125915,10 +141187,10 @@ "tags": [], "tools": [ "trimmomatic", - "hisat2", "deg_annotate", "fastqc", - "stringtie" + "stringtie", + "hisat2" ], "update_time": "2021-09-20", "versions": 0 @@ -125928,17 +141200,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree analysis", - "Sequence read processing", - "Sequencing quality control", - "Phylogenetic analysis", - "Phylogenetic tree generation", - "DNA barcoding", "Visualisation", - "Phylogenetic tree reconstruction", "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic tree analysis", + "Phylogenetic analysis", "Multiple sequence alignment", + "Phylogenetic tree reconstruction", "Sequence analysis", + "Sequence read processing", "Taxonomic classification" ], "edam_topic": [], @@ -125957,10 +141229,10 @@ ], "tools": [ "rbc_mafft", - "iqtree", - "newick_display", "mothur_fastq_info", - "clustalw" + "newick_display", + "clustalw", + "iqtree" ], "update_time": "2021-09-07", "versions": 4 @@ -125970,12 +141242,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "1dd60e57d1d00406", @@ -125988,9 +141260,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "hisat2", "featurecounts", - "hisat2" + "fastqc" ], "update_time": "2021-09-07", "versions": 0 @@ -126000,11 +141272,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly validation", + "Sequence composition calculation", "Visualisation", "Statistical calculation", - "Sequence composition calculation", "Genome assembly", + "Sequence assembly validation", "Sequencing quality control" ], "edam_topic": [], @@ -126018,10 +141290,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "quast", + "shovill", "trimmomatic", - "shovill" + "quast", + "fastqc" ], "update_time": "2021-09-05", "versions": 0 @@ -126044,11 +141316,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffmerge", - "cuffdiff", - "cufflinks", "bowtie2", - "cuffcompare" + "cufflinks", + "cuffcompare", + "cuffdiff", + "cuffmerge" ], "update_time": "2021-09-02", "versions": 3 @@ -126058,9 +141330,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "b04989efde68dee2", @@ -126073,8 +141345,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "featurecounts", "hisat2", + "featurecounts", "trimmomatic" ], "update_time": "2021-09-02", @@ -126096,11 +141368,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffmerge", - "cuffdiff", - "tophat2", "cufflinks", - "cuffcompare" + "tophat2", + "cuffcompare", + "cuffdiff", + "cuffmerge" ], "update_time": "2021-08-17", "versions": 1 @@ -126110,12 +141382,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "6da54816b436dc58", @@ -126128,12 +141400,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "createInterval", - "fastq_dump", "freebayes", "vcfbedintersect", "fastqc", - "bowtie2" + "fastq_dump" ], "update_time": "2021-08-16", "versions": 2 @@ -126154,10 +141426,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "sort1", "table_annovar", - "vcffilter2", "bcftools_plugin_counts", - "sort1", + "vcffilter2", "bcftools_stats", "Grouping1" ], @@ -126171,9 +141443,9 @@ "edam_operation": [ "Sequence contamination filtering", "Statistical calculation", - "Sequencing quality control", "Sequence alignment", "Variant calling", + "Sequencing quality control", "Formatting" ], "edam_topic": [], @@ -126187,14 +141459,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "vcffilter2", - "samtools_view", "freebayes", + "picard_CleanSam", + "picard_MergeSamFiles", "fastp", + "picard_AddOrReplaceReadGroups", + "vcffilter2", "hisat2", - "picard_MergeSamFiles", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "samtools_view" ], "update_time": "2021-08-13", "versions": 0 @@ -126204,13 +141476,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", "Sequence contamination filtering", - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "3f92474cd16ca314", @@ -126223,11 +141495,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "tp_cut_tool", - "fasterq_dump", "fastp", - "Grep1" + "fasterq_dump", + "Grep1", + "bwa_mem", + "tp_cut_tool" ], "update_time": "2021-08-10", "versions": 0 @@ -126253,21 +141525,21 @@ "scanpy" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", + "Filter1", "anndata_import", "scanpy_plot", - "tp_awk_tool", + "tp_tail_tool", "Cut1", - "scanpy_filter", + "anndata_manipulate", "scanpy_inspect", - "scanpy_normalize", - "scanpy_cluster_reduce_dimension", "tp_cat", + "scanpy_normalize", "scanpy_remove_confounders", - "Filter1", "tp_replace_in_column", - "tp_tail_tool" + "scanpy_cluster_reduce_dimension", + "scanpy_filter", + "anndata_inspect", + "tp_awk_tool" ], "update_time": "2021-06-21", "versions": 4 @@ -126277,17 +141549,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "e51aaf4d6b16b4d4", @@ -126300,19 +141572,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "bcftools_stats", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2021-05-30", "versions": 1 @@ -126322,13 +141594,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "2d149545a4920326", @@ -126341,17 +141613,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mothur_pre_cluster", "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_remove_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", + "mothur_pre_cluster", + "mothur_summary_seqs", + "mothur_align_seqs", "mothur_chimera_vsearch", "mothur_filter_seqs", - "mothur_summary_seqs", + "mothur_remove_seqs", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs" ], "update_time": "2021-05-12", "versions": 0 @@ -126361,9 +141633,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "58ce6470337a190d", @@ -126376,12 +141648,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-07", @@ -126392,9 +141664,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "17beb47e45a7690c", @@ -126407,11 +141679,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", + "trimmomatic", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-07", @@ -126422,9 +141694,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "794e7e952003d3d9", @@ -126437,11 +141709,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", + "trimmomatic", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-06", @@ -126495,9 +141767,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "2566f7c6bef19b18", @@ -126510,12 +141782,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", + "tophat2", + "trimmomatic", + "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-06", @@ -126548,9 +141820,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "e7bfa3c733835b22", @@ -126563,12 +141835,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", + "tophat2", + "trimmomatic", + "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-06", @@ -126579,11 +141851,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -126597,12 +141869,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", + "tophat2", + "fastqc", "cutadapt", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-06", @@ -126613,11 +141885,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -126631,12 +141903,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", + "tophat2", + "fastqc", "cutadapt", + "cuffdiff", "cuffmerge" ], "update_time": "2021-05-06", @@ -126661,8 +141933,8 @@ "tags": [], "tools": [ "Filter1", - "cuffdiff", - "hisat2" + "hisat2", + "cuffdiff" ], "update_time": "2021-05-06", "versions": 3 @@ -126715,9 +141987,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Nucleic acid sequence analysis", + "RNA-Seq quantification", "Read summarisation", - "RNA-Seq quantification" + "Nucleic acid sequence analysis" ], "edam_topic": [], "id": "41c09a87c6cd5f75", @@ -126730,10 +142002,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_multijoin_tool", + "htseq_count", "cuffdiff", "featurecounts", - "htseq_count" + "tp_multijoin_tool" ], "update_time": "2021-05-04", "versions": 0 @@ -126754,11 +142026,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2021-04-28", "versions": 1 @@ -126768,11 +142040,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Genome assembly", - "Sequencing quality control" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "ae81cc0e8263d03e", @@ -126789,10 +142061,10 @@ ], "tools": [ "trimmomatic", + "spades", "fastq_paired_end_deinterlacer", - "fastq_dump", "fastqc", - "spades" + "fastq_dump" ], "update_time": "2021-04-22", "versions": 2 @@ -126813,11 +142085,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2021-04-08", "versions": 1 @@ -126827,17 +142099,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "9c0bbf9e1c90cd66", @@ -126850,19 +142122,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2021-04-06", "versions": 0 @@ -126883,14 +142155,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-04-01", "versions": 5 @@ -126914,14 +142186,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-03-31", "versions": 6 @@ -126931,19 +142203,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Multilocus sequence typing", - "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", "Gene prediction", "Genome annotation", "Statistical calculation", - "Coding region prediction" + "Visualisation", + "Genome assembly", + "Sequence assembly visualisation", + "Multilocus sequence typing", + "Sequencing quality control", + "Aggregation", + "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "8111bb9bb26bb665", @@ -126961,14 +142233,14 @@ "wgs" ], "tools": [ + "prokka", + "bandage_info", + "fastqc", "abricate", - "mlst", "bandage_image", "quast", - "prokka", - "fastqc", "unicycler", - "bandage_info" + "mlst" ], "update_time": "2021-03-30", "versions": 11 @@ -126978,19 +142250,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Genome assembly", - "Multilocus sequence typing", - "Sequence assembly visualisation", - "Sequence assembly validation", - "Visualisation", - "Antimicrobial resistance prediction", "Gene prediction", "Genome annotation", "Statistical calculation", - "Coding region prediction" + "Visualisation", + "Genome assembly", + "Sequence assembly visualisation", + "Multilocus sequence typing", + "Sequencing quality control", + "Aggregation", + "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "c65bec6c332bf740", @@ -127008,14 +142280,14 @@ "wgs" ], "tools": [ + "prokka", + "bandage_info", + "fastqc", "abricate", - "mlst", "bandage_image", "quast", - "prokka", - "fastqc", "unicycler", - "bandage_info" + "mlst" ], "update_time": "2021-03-30", "versions": 9 @@ -127025,16 +142297,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence trimming", + "Read mapping" ], "edam_topic": [], "id": "0f43ad9dfd0f6d16", @@ -127047,11 +142319,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "samtools_mpileup", + "bcftools_call", "vcffilter2", "trim_galore", - "bcftools_call", + "bwa_mem", "fastqc" ], "update_time": "2021-03-26", @@ -127062,16 +142334,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "Nucleic acid sequence analysis" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d5514e327878b531", @@ -127084,15 +142356,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "htseq_count", "limma_voom", - "tp_cut_tool", + "tp_tail_tool", "trim_galore", - "fastq_dump", - "htseq_count", - "hisat2", "collection_column_join", "fastqc", - "tp_tail_tool" + "tp_cut_tool", + "hisat2", + "fastq_dump" ], "update_time": "2021-03-23", "versions": 4 @@ -127104,16 +142376,16 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Formatting", + "Statistical calculation", "Sequence alignment", - "Variant calling", "Primer removal", - "Read pre-processing", "Sequence trimming", - "Statistical calculation", + "Formatting", + "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "7020413598cc2023", @@ -127136,17 +142408,17 @@ "bcftools" ], "tools": [ - "deeptools_bam_coverage", "bcftools_plugin_color_chrs", - "bwa_mem", - "picard_MarkDuplicates", - "vcffilter2", - "snpSift_extractFields", - "trim_galore", - "snpEff", "freebayes", + "snpEff", + "snpSift_extractFields", + "deeptools_bam_coverage", + "vcffilter2", "bcftools_stats", - "picard_SortSam" + "trim_galore", + "picard_SortSam", + "bwa_mem", + "picard_MarkDuplicates" ], "update_time": "2021-03-18", "versions": 5 @@ -127156,11 +142428,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control", "Read mapping" ], @@ -127175,9 +142447,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "bowtie2", "trim_galore", - "bowtie2" + "fastqc" ], "update_time": "2021-03-16", "versions": 13 @@ -127187,11 +142459,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control", "Read mapping" ], @@ -127206,9 +142478,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "bowtie2", "trim_galore", - "bowtie2" + "fastqc" ], "update_time": "2021-03-16", "versions": 3 @@ -127229,11 +142501,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-03-15", "versions": 1 @@ -127257,14 +142529,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-03-11", "versions": 4 @@ -127285,9 +142557,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "CONVERTER_interval_to_bed_0", + "Grouping1", "gops_intersect_1", - "Grouping1" + "CONVERTER_interval_to_bed_0" ], "update_time": "2021-03-11", "versions": 0 @@ -127308,14 +142580,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-03-09", "versions": 13 @@ -127325,17 +142597,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "725f7ffa1cffa069", @@ -127348,13 +142620,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "freebayes", + "picard_AddOrReplaceReadGroups", + "bwa_mem", "fastqc", - "bamFilter", - "picard_AddOrReplaceReadGroups" + "bamFilter" ], "update_time": "2021-03-07", "versions": 0 @@ -127366,16 +142638,16 @@ ], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Read summarisation", + "Statistical calculation", + "Nucleic acid sequence analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Nucleic acid sequence analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Read mapping" ], "edam_topic": [], "id": "e04f443a8ceca0d2", @@ -127396,14 +142668,14 @@ "collections" ], "tools": [ - "samtools_flagstat", - "trim_galore", - "featurecounts", "htseq_count", + "bowtie2", "samtools_stats", + "featurecounts", + "trim_galore", "collection_column_join", "fastqc", - "bowtie2" + "samtools_flagstat" ], "update_time": "2021-03-01", "versions": 5 @@ -127413,15 +142685,15 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "88d0b64011c3148c", @@ -127439,20 +142711,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-02-22", "versions": 1 @@ -127462,15 +142734,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "5a610d5a42d50cf3", @@ -127486,17 +142758,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-02-22", "versions": 1 @@ -127506,14 +142778,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "d4ea6cdd40522eb1", @@ -127530,22 +142802,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-02-22", "versions": 1 @@ -127556,11 +142828,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "c092a3631d68ce38", @@ -127576,15 +142848,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-02-22", "versions": 1 @@ -127608,23 +142880,23 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", - "tp_split_on_column", - "Add_a_column1", "cat1", - "tp_sort_header_tool", - "collapse_dataset", + "Filter1", + "Add_a_column1", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", + "tp_tail_tool", "tp_head_tool", - "Filter1", + "tp_sort_header_tool", + "tp_easyjoin_tool", "snpSift_filter", - "tp_tail_tool" + "replace_column_with_key_value_file", + "datamash_ops", + "tp_split_on_column" ], "update_time": "2021-02-22", "versions": 1 @@ -127634,13 +142906,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "b2e81f82ccf3afd6", @@ -127654,10 +142926,10 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", - "hisat2", "collection_column_join", - "fastqc" + "fastqc", + "hisat2", + "fastq_dump" ], "update_time": "2021-02-03", "versions": 0 @@ -127667,10 +142939,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "c64719e91e7346a2", @@ -127692,25 +142964,25 @@ "splice_variants" ], "tools": [ - "fastq_quality_trimmer", - "tophat2", - "hgv_david", + "Grep1", + "join1", "fastqc", - "fastq_groomer", - "comp1", + "cuffmerge", + "Filter1", "sort1", - "Show beginning1", - "cshl_fastx_clipper", "Add_a_column1", - "join1", - "cuffdiff", + "tophat2", + "Show beginning1", "Convert characters1", + "comp1", + "cuffdiff", "picard_MarkDuplicates", - "Cut1", + "fastq_quality_trimmer", "cufflinks", - "Filter1", - "Grep1", - "cuffmerge" + "cshl_fastx_clipper", + "hgv_david", + "Cut1", + "fastq_groomer" ], "update_time": "2021-01-28", "versions": 54 @@ -127734,14 +143006,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-01-21", "versions": 5 @@ -127762,14 +143034,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2021-01-21", "versions": 4 @@ -127779,16 +143051,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "02755c14619242da", @@ -127802,20 +143074,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2021-01-21", "versions": 0 @@ -127825,16 +143097,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2dd4f04c7de7d173", @@ -127848,21 +143120,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2021-01-07", "versions": 0 @@ -127872,16 +143144,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "17a7ff756d37a437", @@ -127895,23 +143167,23 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", "snpEff_download", - "tp_sort_header_tool", - "vcffilter2", - "Summary_Statistics1", + "freebayes", "table_annovar", "snpEff", - "freebayes", - "samtool_filter2", - "fastqc", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "tp_sort_header_tool", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2021-01-06", "versions": 0 @@ -127921,16 +143193,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d7049965ca7d8ea9", @@ -127944,21 +143216,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2021-01-05", "versions": 0 @@ -127968,10 +143240,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Genome annotation", - "Scaffolding", "Genome assembly", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -127986,9 +143258,9 @@ "tags": [], "tools": [ "fasta-stats", - "maker", + "jcvi_gff_stats", "busco", - "jcvi_gff_stats" + "maker" ], "update_time": "2021-01-03", "versions": 0 @@ -127998,16 +143270,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "76247065c01f01d1", @@ -128021,21 +143293,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats" + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2021-01-03", "versions": 2 @@ -128045,17 +143317,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", "Primer removal", + "Sequence annotation", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6d0a3f36d2736087", @@ -128068,22 +143340,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gprofiler_gost", "limma_voom", - "tp_cut_tool", - "Cut1", + "Filter1", "gffread", - "trim_galore", + "gprofiler_gost", "tp_find_and_replace", - "fasterq_dump", + "tp_tail_tool", "salmon", + "fasterq_dump", + "trim_galore", + "Grep1", + "column_order_header_sort", "collection_column_join", - "__RELABEL_FROM_FILE__", "fastqc", - "column_order_header_sort", - "Filter1", - "Grep1", - "tp_tail_tool" + "tp_cut_tool", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2020-12-21", "versions": 4 @@ -128093,16 +143365,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "9f5f2e309a3ea50c", @@ -128115,22 +143387,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "samtools_idxstats", + "trimmomatic", + "picard_CollectInsertSizeMetrics", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2020-12-15", "versions": 1 @@ -128151,10 +143423,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_cut_tool", - "join1", "gops_join_1", - "Grouping1" + "Grouping1", + "join1", + "tp_cut_tool" ], "update_time": "2020-12-11", "versions": 1 @@ -128164,17 +143436,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", + "Mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "0a57740c68e85e21", @@ -128187,22 +143459,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bedtools_genomecoveragebed", - "bwa_mem", - "picard_ValidateSamFile", - "sam_merge2", - "bamleftalign", - "picard_MarkDuplicates", + "Filter1", + "freebayes", + "bcftools_merge", "bcftools_norm", + "qualimap_bamqc", + "sam_merge2", + "picard_ValidateSamFile", "vcffilter2", - "bcftools_merge", + "gops_join_1", "fastq_paired_end_interlacer", - "freebayes", - "Filter1", - "qualimap_bamqc", + "bwa_mem", "bamFilter", - "gops_join_1", - "picard_FixMateInformation" + "bedtools_genomecoveragebed", + "bamleftalign", + "picard_FixMateInformation", + "picard_MarkDuplicates" ], "update_time": "2020-12-01", "versions": 0 @@ -128212,9 +143484,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "947340358dd268ea", @@ -128227,8 +143499,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "cshl_fastq_quality_filter", + "fastqc", "cshl_fastx_artifacts_filter", "trimmomatic" ], @@ -128240,9 +143512,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "c446105e87750aa2", @@ -128256,8 +143528,8 @@ "tags": [], "tools": [ "fastqc", - "fastq_groomer", - "fastq_paired_end_interlacer" + "fastq_paired_end_interlacer", + "fastq_groomer" ], "update_time": "2020-12-01", "versions": 0 @@ -128267,9 +143539,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "812bc1b7a52f4f6f", @@ -128282,8 +143554,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "featurecounts", - "hisat2" + "hisat2", + "featurecounts" ], "update_time": "2020-11-17", "versions": 7 @@ -128294,10 +143566,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "94da3d448bb8a137", @@ -128311,8 +143583,8 @@ "tags": [], "tools": [ "EMBOSS: matcher52", - "filter_by_fasta_ids", - "rbc_splitfasta" + "rbc_splitfasta", + "filter_by_fasta_ids" ], "update_time": "2020-11-10", "versions": 4 @@ -128322,16 +143594,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5ce5b3061c6afd82", @@ -128344,15 +143616,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "bwa", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", "fastqc", - "bedtools_coveragebed" + "bwa", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2020-11-05", "versions": 2 @@ -128362,16 +143634,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "71f129d96b81851e", @@ -128384,15 +143656,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", + "bwa_mem", "fastqc", - "bedtools_coveragebed" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2020-11-02", "versions": 0 @@ -128417,8 +143689,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2020-10-07", "versions": 1 @@ -128428,12 +143700,12 @@ "creators": [], "doi": "", "edam_operation": [ + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", "Sequence alignment", - "Variant calling" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "ae359a3c83f2e19f", @@ -128446,9 +143718,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bcftools_plugin_counts", "freebayes", - "bwa_mem", - "bcftools_plugin_counts" + "bwa_mem" ], "update_time": "2020-10-06", "versions": 1 @@ -128458,13 +143730,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "d97a88a8f9061e25", @@ -128477,11 +143749,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2020-09-28", "versions": 37 @@ -128491,13 +143763,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "e22ea88bc0fdc146", @@ -128510,11 +143782,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "fastq_dump", + "trimmomatic", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2020-09-23", "versions": 2 @@ -128535,12 +143807,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", - "tp_cut_tool", - "join1", "Grouping1", - "Show beginning1", - "gops_join_1" + "join1", + "tp_cut_tool" ], "update_time": "2020-09-03", "versions": 0 @@ -128550,17 +143822,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence trimming", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "f1a9667c0b0999f4", @@ -128573,15 +143845,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "samtools_flagstat", + "allele_counts_1", "naive_variant_caller", + "samtools_rmdup", "trimmomatic", - "allele_counts_1", "trim_galore", - "samtools_rmdup", - "fastqc" + "bwa_mem", + "fastqc", + "bamleftalign", + "samtools_flagstat" ], "update_time": "2020-08-25", "versions": 4 @@ -128591,10 +143863,10 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", + "RNA-Seq quantification", "Read summarisation", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "0a009cf9e88171f1", @@ -128621,8 +143893,8 @@ ], "tools": [ "limma_voom", - "featurecounts", - "hisat2" + "hisat2", + "featurecounts" ], "update_time": "2020-08-08", "versions": 35 @@ -128645,22 +143917,22 @@ "imported" ], "tools": [ - "tabular_to_fastq", - "fastq_groomer", - "fasta2tab", - "fastq_to_fasta_python", - "cshl_fastx_reverse_complement", - "Grep1", - "tab2fasta", - "tp_find_and_replace", - "join1", - "tp_replace_in_line", "fastq_to_tabular", "sort1", - "cshl_fastx_collapser", + "fastq_to_fasta_python", "Show beginning1", "tp_head_tool", - "fastq_manipulation" + "tp_find_and_replace", + "tab2fasta", + "tp_replace_in_line", + "fasta2tab", + "Grep1", + "fastq_manipulation", + "join1", + "tabular_to_fastq", + "cshl_fastx_reverse_complement", + "cshl_fastx_collapser", + "fastq_groomer" ], "update_time": "2020-07-21", "versions": 6 @@ -128670,9 +143942,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Multiple sequence alignment", "Statistical calculation", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Multiple sequence alignment" ], "edam_topic": [], "id": "a46ad0b9240d1a13", @@ -128685,19 +143957,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "kc-align", - "sarscov2summary", - "Cut1", "sarscov2formatter", - "rapidnj", "param_value_from_file", + "sarscov2summary", + "rapidnj", "hyphy_meme", - "hyphy_prime", + "hyphy_fel", + "split_file_to_collection", "Remove beginning1", + "kc-align", "hyphy_slac", - "__RELABEL_FROM_FILE__", - "split_file_to_collection", - "hyphy_fel" + "hyphy_prime", + "Cut1", + "__RELABEL_FROM_FILE__" ], "update_time": "2020-07-10", "versions": 30 @@ -128707,8 +143979,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -128722,10 +143994,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "freebayes", - "samtools_stats", "bowtie2", - "lofreq_call" + "lofreq_call", + "samtools_stats", + "freebayes" ], "update_time": "2020-06-25", "versions": 1 @@ -128736,12 +144008,12 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Sequence alignment", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "7551458d929355c2", @@ -128756,9 +144028,9 @@ "tools": [ "stringtie_merge", "multiqc", - "hisat2", "fastqc", - "stringtie" + "stringtie", + "hisat2" ], "update_time": "2020-06-22", "versions": 1 @@ -128779,8 +144051,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_awk_tool", - "tp_replace_in_line" + "tp_replace_in_line", + "tp_awk_tool" ], "update_time": "2020-06-18", "versions": 4 @@ -128790,15 +144062,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Differential gene expression analysis", "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9bace540b35b1e61", @@ -128820,12 +144092,12 @@ "deseq2" ], "tools": [ - "trimmomatic", + "bowtie2", "featurecounts", + "trimmomatic", "multiqc", "fastqc", - "deseq2", - "bowtie2" + "deseq2" ], "update_time": "2020-06-17", "versions": 7 @@ -128835,12 +144107,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment" + "Data handling" ], "edam_topic": [], "id": "0f43fdfe1824e9d7", @@ -128853,14 +144125,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_fastx", - "samtools_view", - "fastq_dump", - "picard_DownsampleSam", "cshl_fastq_quality_filter", "samtool_filter2", + "samtools_fastx", + "fastqc", "hisat2", - "fastqc" + "fastq_dump", + "samtools_view", + "picard_DownsampleSam" ], "update_time": "2020-06-11", "versions": 6 @@ -128870,8 +144142,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", "RNA-Seq analysis", + "Sequence annotation", "Sequence alignment", "Transcriptome assembly" ], @@ -128886,10 +144158,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gffcompare", "stringtie_merge", "stringtie", - "hisat2" + "hisat2", + "gffcompare" ], "update_time": "2020-06-05", "versions": 4 @@ -128899,12 +144171,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", "Sequence contamination filtering", - "Read mapping", + "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Read mapping" ], "edam_topic": [], "id": "92875b13082b5568", @@ -128917,10 +144189,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "fastp", + "bowtie2", "hisat2", - "bowtie2" + "fastp", + "fastqc" ], "update_time": "2020-06-01", "versions": 0 @@ -128930,17 +144202,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "1e53fcd07ae5d859", @@ -128953,19 +144225,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-05-29", "versions": 0 @@ -128975,17 +144247,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "cb03300161109123", @@ -128998,21 +144270,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", + "snpEff", + "picard_CleanSam", + "snpSift_extractFields", "sam_merge2", - "picard_MarkDuplicates", - "tp_sort_header_tool", + "picard_AddOrReplaceReadGroups", "vcffilter2", - "snpSift_extractFields", - "snpEff", - "freebayes", - "Remove beginning1", "charts", + "Remove beginning1", + "tp_sort_header_tool", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-05-28", "versions": 0 @@ -129022,17 +144294,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "0a89328e6d28dd07", @@ -129045,19 +144317,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-05-12", "versions": 0 @@ -129078,8 +144350,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "__MERGE_COLLECTION__", - "collapse_dataset" + "collapse_dataset", + "__MERGE_COLLECTION__" ], "update_time": "2020-05-05", "versions": 1 @@ -129090,9 +144362,9 @@ "doi": "", "edam_operation": [ "Statistical calculation", - "Multiple sequence alignment", + "Phylogenetic analysis", "Sequence analysis", - "Phylogenetic analysis" + "Multiple sequence alignment" ], "edam_topic": [], "id": "e1cc0886cd27b92e", @@ -129105,19 +144377,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "kc-align", - "sarscov2summary", - "Cut1", "sarscov2formatter", - "hyphy_meme", "param_value_from_file", - "hyphy_prime", + "sarscov2summary", + "hyphy_meme", + "hyphy_fel", + "split_file_to_collection", "Remove beginning1", - "iqtree", + "kc-align", "hyphy_slac", + "hyphy_prime", + "Cut1", "__RELABEL_FROM_FILE__", - "split_file_to_collection", - "hyphy_fel" + "iqtree" ], "update_time": "2020-05-04", "versions": 3 @@ -129138,12 +144410,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2020-05-03", "versions": 0 @@ -129153,14 +144425,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", - "Read mapping", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Validation", "Sequencing quality control", - "Validation" + "Read mapping", + "Primer removal" ], "edam_topic": [], "id": "ae523fe6c9183e58", @@ -129173,10 +144445,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "samtools_stats", "multiqc", "fastqc", - "bowtie2", "cutadapt" ], "update_time": "2020-05-02", @@ -129199,8 +144471,8 @@ "tags": [], "tools": [ "tp_sorted_uniq", - "Grouping1", - "column_remove_by_header" + "column_remove_by_header", + "Grouping1" ], "update_time": "2020-04-22", "versions": 4 @@ -129210,15 +144482,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Genome indexing", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Sequence file editing", - "Generation" + "Generation", + "Genome indexing", + "Sequence composition calculation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "7610b7797d71993a", @@ -129231,14 +144503,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "samtools_rmdup", + "snpEff", "trimmomatic", "seqtk_sample", - "samtools_rmdup", "bcftools_call", "samtools_sort", - "snpEff", "bcftools_filter", + "bwa_mem", "fastqc", "bcftools_mpileup" ], @@ -129261,11 +144533,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", + "gops_join_1", "tp_sort_header_tool", - "Cut1", "Grouping1", - "gops_join_1" + "tp_easyjoin_tool", + "Cut1" ], "update_time": "2020-04-06", "versions": 0 @@ -129286,12 +144558,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2020-03-29", "versions": 0 @@ -129313,10 +144585,10 @@ "tags": [], "tools": [ "sort1", - "Grouping1", - "Show beginning1", "Filter1", - "gops_join_1" + "Show beginning1", + "gops_join_1", + "Grouping1" ], "update_time": "2020-03-29", "versions": 1 @@ -129337,12 +144609,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_cut_tool", - "join1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "tp_cut_tool" ], "update_time": "2020-03-22", "versions": 1 @@ -129363,12 +144635,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_cut_tool", - "join1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "tp_cut_tool" ], "update_time": "2020-03-21", "versions": 1 @@ -129378,13 +144650,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "413d7e5aa7378cf1", @@ -129397,11 +144669,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "rna_star", - "featurecounts", "htseq_count", - "fastqc" + "featurecounts", + "trimmomatic", + "fastqc", + "rna_star" ], "update_time": "2020-03-06", "versions": 6 @@ -129411,9 +144683,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", "Formatting", - "Variant calling", - "Statistical calculation" + "Variant calling" ], "edam_topic": [], "id": "4cbb8181cfdf55d9", @@ -129429,11 +144701,11 @@ "variant" ], "tools": [ - "varscan_mpileup", "samtools_mpileup", - "samtools_rmdup", "freebayes", + "samtools_rmdup", "samtool_filter2", + "varscan_mpileup", "lofreq_call", "picard_FixMateInformation" ], @@ -129445,10 +144717,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Taxonomic classification", - "Sequencing quality control" + "Statistical calculation", + "Sequencing quality control", + "Taxonomic classification" ], "edam_topic": [], "id": "a89e1018a00b883c", @@ -129462,10 +144734,10 @@ "tags": [], "tools": [ "trimmomatic", - "kraken", + "kraken-translate", "kraken-report", "fastqc", - "kraken-translate" + "kraken" ], "update_time": "2020-02-28", "versions": 0 @@ -129475,17 +144747,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "470b41d0e43bb46b", @@ -129498,20 +144770,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", + "snpEff", + "picard_CleanSam", + "snpSift_extractFields", "sam_merge2", - "picard_MarkDuplicates", - "tp_sort_header_tool", + "picard_AddOrReplaceReadGroups", "vcffilter2", - "snpSift_extractFields", - "snpEff", - "freebayes", + "tp_sort_header_tool", "Remove beginning1", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-02-26", "versions": 3 @@ -129521,19 +144793,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", - "Pairwise sequence alignment", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", + "Pairwise sequence alignment", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "4458439388155d92", @@ -129546,15 +144818,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "minimap2", "samtool_filter2", - "fastp", + "samtools_fastx", + "picard_MergeSamFiles", "multiqc", - "fastqc" + "fastp", + "nanoplot", + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-02-23", "versions": 2 @@ -129564,10 +144836,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment", "Formatting", - "Phylogenetic tree generation (from molecular sequences)" + "Multiple sequence alignment" ], "edam_topic": [], "id": "be54e57345ce7ca5", @@ -129580,15 +144852,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasttree", - "ncbi_acc_download", - "collapse_dataset", "picard_NormalizeFasta", - "Cut1", - "tp_sed_tool", "rbc_mafft", + "fasttree", + "collapse_dataset", "Remove beginning1", - "Convert characters1" + "Convert characters1", + "tp_sed_tool", + "ncbi_acc_download", + "Cut1" ], "update_time": "2020-02-21", "versions": 8 @@ -129598,9 +144870,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "5039ae2c81d0aba8", @@ -129613,10 +144885,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2020-02-21", "versions": 5 @@ -129626,15 +144898,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Statistical calculation", "Sequence alignment", "Phylogenetic tree generation (from molecular sequences)", - "Statistical calculation", - "Global alignment", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "2d1ca299c1b058f6", @@ -129647,12 +144919,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "rbc_mafft", + "EMBOSS: transeq101", "fasttree", "hyphy_gard", - "EMBOSS: transeq101", - "rbc_mafft", - "hyphy_absrel", - "EMBOSS: tranalign100" + "EMBOSS: tranalign100", + "hyphy_absrel" ], "update_time": "2020-02-21", "versions": 2 @@ -129662,12 +144934,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "956987e628530c79", @@ -129680,8 +144952,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "EMBOSS: transeq101", "rbc_mafft", + "EMBOSS: transeq101", "EMBOSS: tranalign100" ], "update_time": "2020-02-20", @@ -129692,12 +144964,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "f737593a1db217c8", @@ -129710,8 +144982,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "EMBOSS: transeq101", "rbc_mafft", + "EMBOSS: transeq101", "EMBOSS: tranalign100" ], "update_time": "2020-02-18", @@ -129722,11 +144994,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Multiple sequence alignment", "Sequence analysis", + "Sequence alignment", + "Read mapping", "Phylogenetic analysis", - "Sequence alignment" + "Multiple sequence alignment" ], "edam_topic": [], "id": "23212ae74fc2d2b5", @@ -129739,16 +145011,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "ncbi_acc_download", + "Filter1", + "rbc_mafft", "collapse_dataset", + "tp_replace_in_line", + "lastz_wrapper_2", + "ncbi_acc_download", "Cut1", "__FILTER_FROM_FILE__", - "lastz_wrapper_2", "snpEff_build_gb", - "tp_replace_in_line", - "rbc_mafft", - "iqtree", - "Filter1" + "iqtree" ], "update_time": "2020-02-16", "versions": 4 @@ -129758,14 +145030,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Sequencing quality control", "Formatting", + "Sequence composition calculation", + "Sequence alignment analysis", "Variant calling", - "Statistical calculation" + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "0d8eb75d28fa7df2", @@ -129779,19 +145051,19 @@ "tags": [], "tools": [ "bowtie2", + "Filter1", + "freebayes", + "samtool_filter2", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", - "samtool_filter2", "Grouping1", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-01-16", "versions": 0 @@ -129823,11 +145095,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Formatting", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "69363bab20c5ca6c", @@ -129840,16 +145112,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gatk_variant_filtration", "gatk_table_recalibration", - "bwa_mem", - "picard_MarkDuplicates", "trimmomatic", - "gatk_variant_select", "gatk_count_covariates", "samtools_sort", - "gatk_variant_filtration", + "gatk_variant_select", "gatk_analyze_covariates", - "gatk_unified_genotyper" + "gatk_unified_genotyper", + "bwa_mem", + "picard_MarkDuplicates" ], "update_time": "2019-11-24", "versions": 2 @@ -129859,17 +145131,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Variant calling", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "49f8b32c3206f76c", @@ -129886,20 +145158,20 @@ "human" ], "tools": [ - "bwa_mem", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "sam_merge2", - "picard_MarkDuplicates", + "picard_AddOrReplaceReadGroups", "vcffilter2", - "table_annovar", - "bwa", - "freebayes", - "sort1", "Remove beginning1", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "bwa", + "picard_MarkDuplicates" ], "update_time": "2019-11-22", "versions": 7 @@ -129922,8 +145194,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "naive_variant_caller", "bowtie2", + "naive_variant_caller", "varscan" ], "update_time": "2019-11-18", @@ -129945,11 +145217,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2019-10-27", "versions": 2 @@ -129959,15 +145231,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence composition calculation", + "RNA-Seq quantification", + "Read summarisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9c022f4028de0bc6", @@ -129980,14 +145252,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gffcompare", - "tp_sort_header_tool", - "trimmomatic", "featurecounts", - "hisat2", - "fastqc", + "trimmomatic", "tp_head_tool", - "stringtie" + "stringtie", + "tp_sort_header_tool", + "fastqc", + "gffcompare", + "hisat2" ], "update_time": "2019-10-14", "versions": 4 @@ -129997,17 +145269,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "529c6c68df669c51", @@ -130020,19 +145292,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2019-10-06", "versions": 0 @@ -130042,11 +145314,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", - "Sequence alignment" + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "a86b1f1682bb4a62", @@ -130059,9 +145331,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "htseq_count", "hisat2", - "htseq_count" + "fastqc" ], "update_time": "2019-09-28", "versions": 1 @@ -130102,14 +145374,14 @@ "tags": [], "tools": [ "cat1", + "sort1", "sam_bw_filter", - "fastq_groomer", - "gatk_realigner_target_creator", "gatk_indel_realigner", - "sort1", - "bwa_wrapper", + "Grep1", "gatk_unified_genotyper", - "Grep1" + "bwa_wrapper", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2019-09-24", "versions": 0 @@ -130130,11 +145402,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Count1", - "datamash_ops", "sort1", + "Grep1", "Convert characters1", - "Grep1" + "Count1", + "datamash_ops" ], "update_time": "2019-08-28", "versions": 3 @@ -130144,16 +145416,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "fb903de4aa4d5090", @@ -130167,11 +145439,11 @@ "tags": [], "tools": [ "featurecounts", - "fastq_dump", - "hisat2", "multiqc", "collection_column_join", "fastqc", + "hisat2", + "fastq_dump", "deseq2" ], "update_time": "2019-08-22", @@ -130203,8 +145475,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "fe764741eb374b87", @@ -130227,9 +145499,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "cd431e5f912d3616", @@ -130242,13 +145514,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "featurecounts", + "trimmomatic", "cshl_fastx_barcode_splitter", - "__ZIP_COLLECTION__", "__FILTER_FAILED_DATASETS__", - "trimmomatic", - "featurecounts", - "hisat2", - "collection_column_join" + "__ZIP_COLLECTION__", + "collection_column_join", + "hisat2" ], "update_time": "2019-08-07", "versions": 9 @@ -130258,16 +145530,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Mapping", + "Statistical calculation", "Sequencing quality control", + "Sequence composition calculation", "Gene regulatory network analysis", - "Statistical calculation", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "7643e66a9b4e9c11", @@ -130280,25 +145552,25 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "deeptools_compute_matrix", - "Extract genomic DNA 1", - "deeptools_multi_bigwig_summary", "deeptools_plot_correlation", - "macs2_callpeak", - "deeptools_plot_pca", - "deeptools_bigwig_compare", + "bed2gff1", "chipseeker", + "trimmomatic", "deeptools_bam_coverage", + "deeptools_bigwig_compare", + "fastqc", + "resize_coordinate_window", + "bowtie2", + "multiqc", "deeptools_plot_heatmap", - "trimmomatic", + "deeptools_compute_matrix", + "Extract genomic DNA 1", + "deeptools_plot_pca", + "macs2_callpeak", "deeptools_plot_fingerprint", - "bed2gff1", "fastq_dump", - "resize_coordinate_window", - "multiqc", - "bowtie2", - "bedtools_intersectbed" + "bedtools_intersectbed", + "deeptools_multi_bigwig_summary" ], "update_time": "2019-07-30", "versions": 91 @@ -130308,9 +145580,9 @@ "creators": [], "doi": "", "edam_operation": [ + "RNA-Seq quantification", "Read summarisation", - "Sequence alignment", - "RNA-Seq quantification" + "Sequence alignment" ], "edam_topic": [], "id": "4a50ce0e9f4d4bb8", @@ -130323,10 +145595,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "featurecounts", "hisat2", - "trimmomatic", - "collection_column_join" + "collection_column_join", + "featurecounts", + "trimmomatic" ], "update_time": "2019-07-30", "versions": 16 @@ -130336,19 +145608,19 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", "Peak calling", - "Gene regulatory network analysis", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Read pre-processing", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Data handling" ], "edam_topic": [], "id": "9b5ae15bb9aaba48", @@ -130364,14 +145636,14 @@ "hg19" ], "tools": [ - "bamFilter", - "sam_merge2", - "samtools_sort", + "bowtie2", + "macs2_callpeak", "samtool_filter2", + "samtools_sort", + "sam_merge2", "multiqc", "fastqc", - "macs2_callpeak", - "bowtie2", + "bamFilter", "cutadapt" ], "update_time": "2019-07-26", @@ -130382,13 +145654,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Formatting", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "80b12b6e7ac8861f", @@ -130401,11 +145673,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", "samtools_mpileup", + "freebayes", "varscan", - "freebayes" + "bwa_mem", + "picard_MarkDuplicates" ], "update_time": "2019-06-22", "versions": 6 @@ -130415,10 +145687,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "1e1a299825f27f11", @@ -130436,18 +145708,18 @@ "fastq" ], "tools": [ - "tp_easyjoin_tool", + "fastq_to_tabular", "tabular_to_fastq", "wc_gnu", - "tp_cut_tool", "tp_find_and_replace", - "tp_sorted_uniq", "tp_replace_in_line", - "fastq_to_tabular", - "random_lines1", - "addValue", "multiqc", - "fastqc" + "random_lines1", + "tp_easyjoin_tool", + "fastqc", + "tp_cut_tool", + "tp_sorted_uniq", + "addValue" ], "update_time": "2019-06-12", "versions": 8 @@ -130457,9 +145729,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -130473,11 +145745,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", "samtools_mpileup", "varscan", - "vcfcombine" + "bwa_mem", + "vcfcombine", + "fastq_groomer" ], "update_time": "2019-05-30", "versions": 3 @@ -130529,8 +145801,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation" ], "edam_topic": [], "id": "667b57893268d96e", @@ -130553,9 +145825,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -130580,16 +145852,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "Nucleic acid sequence analysis" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "204d0da8a023d7da", @@ -130602,16 +145874,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "htseq_count", "limma_voom", - "tp_cut_tool", - "Cut1", + "tp_tail_tool", "trim_galore", - "fastq_dump", - "htseq_count", - "hisat2", "collection_column_join", "fastqc", - "tp_tail_tool" + "tp_cut_tool", + "hisat2", + "Cut1", + "fastq_dump" ], "update_time": "2019-05-08", "versions": 10 @@ -130621,16 +145893,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", + "Nucleic acid sequence analysis", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", - "Nucleic acid sequence analysis" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "b3823d276917baf0", @@ -130643,15 +145915,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "htseq_count", "limma_voom", - "tp_cut_tool", + "tp_tail_tool", "trim_galore", - "fastq_dump", - "htseq_count", - "hisat2", "collection_column_join", "fastqc", - "tp_tail_tool" + "tp_cut_tool", + "hisat2", + "fastq_dump" ], "update_time": "2019-05-07", "versions": 5 @@ -130661,16 +145933,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming" + "Gene regulatory network analysis", + "Sequence composition calculation", + "Sequence trimming", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ecb279a9114140ab", @@ -130683,10 +145955,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "macs2_callpeak", + "bowtie2", "trim_galore", - "bowtie2" + "macs2_callpeak", + "fastqc" ], "update_time": "2019-05-03", "versions": 11 @@ -130707,12 +145979,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2019-04-28", "versions": 3 @@ -130722,11 +145994,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping" ], "edam_topic": [], "id": "683a0ab042fa34c9", @@ -130739,16 +146011,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gatk_realigner_target_creator", - "fastq_groomer", + "bowtie2", "samtools_mpileup", - "varscan", "samtools_rmdup", - "gatk_indel_realigner", "freebayes", + "gatk_indel_realigner", + "varscan", "gatk_unified_genotyper", "fastqc", - "bowtie2" + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2019-04-25", "versions": 9 @@ -130758,15 +146030,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "RNA-Seq analysis", - "Nucleic acid sequence analysis" + "Sequence composition calculation", + "Sequence trimming", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3f8e0395007c8e9e", @@ -130779,13 +146051,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "limma_voom", - "htseq_count", "cshl_fastq_quality_filter", "fastq_filter", - "hisat2", + "htseq_count", + "limma_voom", + "cutadapt", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2019-04-22", "versions": 3 @@ -130795,16 +146067,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e6a6223ef5ef85a7", @@ -130817,28 +146089,28 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", "fastqc", + "sort1", + "Filter1", "samtools_idxstats", - "vcffilter2", "table_annovar", - "freebayes", - "sort1", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", - "tp_awk_tool", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bedtools_sortbed", "Summary_Statistics1", + "picard_CollectInsertSizeMetrics", + "freebayes", + "bcftools_view", "Cut1", - "samtool_filter2", - "bedtools_sortbed", - "Filter1", - "bedtools_coveragebed", - "bcftools_view" + "tp_awk_tool" ], "update_time": "2019-04-11", "versions": 0 @@ -130848,16 +146120,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "57726b39bbfb0c54", @@ -130870,25 +146142,25 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", "fastqc", + "Filter1", "samtools_idxstats", - "bam_to_sam", - "vcffilter2", "table_annovar", - "freebayes", - "tp_sort_header_tool", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", + "tp_sort_header_tool", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2019-04-04", "versions": 0 @@ -130898,16 +146170,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "0843c6f15eae2f15", @@ -130920,29 +146192,29 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", "fastqc", + "sort1", + "Filter1", "samtools_idxstats", - "bam_to_sam", - "vcffilter2", "table_annovar", - "freebayes", - "sort1", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", - "tp_awk_tool", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", + "bedtools_sortbed", "Summary_Statistics1", + "picard_CollectInsertSizeMetrics", + "freebayes", + "bcftools_view", "Cut1", - "samtool_filter2", - "bedtools_sortbed", - "Filter1", - "bedtools_coveragebed", - "bcftools_view" + "tp_awk_tool" ], "update_time": "2019-04-04", "versions": 0 @@ -130952,13 +146224,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", + "Generation", + "Genome indexing", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "Read mapping", - "Genome indexing", - "Generation", - "Sequence alignment" + "Primer removal", + "Read mapping" ], "edam_topic": [], "id": "eedbd4e9caca6195", @@ -130971,10 +146243,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa", - "trim_galore", "bedtools_bamtofastq", - "bowtie2" + "bowtie2", + "bwa", + "trim_galore" ], "update_time": "2019-04-03", "versions": 2 @@ -130984,16 +146256,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4ed9f54caa932479", @@ -131006,31 +146278,31 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", "fastqc", + "sort1", + "Filter1", "samtools_idxstats", - "vcf2tsv", - "bam_to_sam", - "vcffilter2", "table_annovar", - "tp_cut_tool", - "freebayes", - "sort1", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", - "tp_awk_tool", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", + "bedtools_sortbed", "Summary_Statistics1", + "vcf2tsv", + "picard_CollectInsertSizeMetrics", + "freebayes", + "bcftools_view", + "tp_cut_tool", "Cut1", - "samtool_filter2", - "bedtools_sortbed", - "Filter1", - "bedtools_coveragebed", - "bcftools_view" + "tp_awk_tool" ], "update_time": "2019-04-03", "versions": 0 @@ -131040,9 +146312,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -131056,11 +146328,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "bcftools_consensus", "gatk_variant_filtration", "gatk_unified_genotyper", - "fastq_masker_by_quality" + "fastq_masker_by_quality", + "bwa_mem" ], "update_time": "2019-04-02", "versions": 15 @@ -131070,16 +146342,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "049e6609da2b67c4", @@ -131092,25 +146364,25 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", + "snpEff_databases", "fastqc", + "sort1", + "Filter1", "samtools_idxstats", - "bam_to_sam", - "vcffilter2", "table_annovar", - "freebayes", - "sort1", - "snpEff_databases", - "snpEff_download", - "snpEff", + "vcffilter2", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", "Summary_Statistics1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2019-04-02", "versions": 0 @@ -131120,18 +146392,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Sequence composition calculation", + "Sequence alignment analysis", + "Generation", "Genome indexing", - "Generation" + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "41efc922cf146e0c", @@ -131144,11 +146416,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa", - "trim_galore", "samtools_rmdup", + "trim_galore", "fastqc", - "bamFilter" + "bamFilter", + "bwa" ], "update_time": "2019-04-01", "versions": 7 @@ -131158,18 +146430,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Formatting", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", - "Genome indexing", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Sequence trimming", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "958f78270fc8f55c", @@ -131182,18 +146454,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_MarkDuplicates", - "trimmomatic", "bcftools_consensus", - "bwa", - "trim_galore", "gatk_variant_filtration", "samtool_filter2", + "picard_CleanSam", + "trimmomatic", "multiqc", - "fastq_masker_by_quality", + "trim_galore", "gatk_unified_genotyper", + "fastq_masker_by_quality", "fastqc", - "picard_CleanSam" + "bwa", + "picard_MarkDuplicates" ], "update_time": "2019-03-27", "versions": 11 @@ -131203,16 +146475,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ebbcdc389aad0eb8", @@ -131225,29 +146497,29 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", "fastqc", + "sort1", + "Filter1", "samtools_idxstats", - "bam_to_sam", - "vcffilter2", "table_annovar", - "freebayes", - "sort1", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", - "tp_awk_tool", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", + "bam_to_sam", + "bedtools_sortbed", "Summary_Statistics1", + "picard_CollectInsertSizeMetrics", + "freebayes", + "bcftools_view", "Cut1", - "samtool_filter2", - "bedtools_sortbed", - "Filter1", - "bedtools_coveragebed", - "bcftools_view" + "tp_awk_tool" ], "update_time": "2019-03-26", "versions": 0 @@ -131257,14 +146529,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "RNA-Seq quantification" + "Primer removal" ], "edam_topic": [], "id": "48adcc44fe62a99c", @@ -131277,12 +146549,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "trim_galore", - "featurecounts", + "bowtie_wrapper", "fastq_filter", + "featurecounts", + "trim_galore", "fastqc", - "bowtie_wrapper" + "fastq_groomer" ], "update_time": "2019-03-25", "versions": 19 @@ -131292,14 +146564,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", "Sequencing quality control", "Formatting", + "Sequence composition calculation", + "Sequence alignment analysis", "Variant calling", - "Statistical calculation" + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "528ed34505b1a993", @@ -131313,17 +146585,17 @@ "tags": [], "tools": [ "bowtie2", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2019-03-22", "versions": 0 @@ -131336,9 +146608,9 @@ "Visualisation", "Sequence clustering", "Sequence read processing", + "DNA barcoding", "Sequencing quality control", "Phylogenetic analysis", - "DNA barcoding", "Taxonomic classification" ], "edam_topic": [], @@ -131384,11 +146656,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Formatting", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "775e67dc75f741b8", @@ -131401,8 +146673,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "picard_MarkDuplicates", + "bwa_mem", "trimmomatic" ], "update_time": "2019-03-08", @@ -131426,12 +146698,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_awk_tool", - "Cut1", "tp_cut_tool", + "bcftools_view", "bedtools_sortbed", "vcf2tsv", - "bcftools_view" + "Cut1", + "tp_awk_tool" ], "update_time": "2019-03-07", "versions": 8 @@ -131441,16 +146713,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5fa548beeb1411f2", @@ -131464,21 +146736,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2019-03-05", "versions": 0 @@ -131488,16 +146760,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "c95fc8692a886a59", @@ -131511,21 +146783,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2019-03-04", "versions": 0 @@ -131535,16 +146807,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "31acbfc6d3775846", @@ -131558,21 +146830,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "table_annovar", + "Filter1", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "table_annovar", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2019-03-04", "versions": 1 @@ -131582,16 +146854,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "af5acb5dd7bfac56", @@ -131605,21 +146877,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2019-03-04", "versions": 0 @@ -131652,16 +146924,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "415c7152cb78e86f", @@ -131683,25 +146955,25 @@ "snpeff" ], "tools": [ - "picard_CollectInsertSizeMetrics", + "samtool_filter2", + "trimmomatic", + "snpEff_databases", "fastqc", + "Filter1", "samtools_idxstats", - "vcf2tsv", - "vcffilter2", "table_annovar", - "freebayes", - "snpEff_databases", - "snpEff_download", + "vcffilter2", "bcftools_plugin_counts", - "snpEff", "bwa_mem", "samtools_flagstat", "picard_MarkDuplicates", - "trimmomatic", + "bedtools_coveragebed", + "snpEff", + "snpEff_download", "Count1", - "samtool_filter2", - "Filter1", - "bedtools_coveragebed" + "vcf2tsv", + "picard_CollectInsertSizeMetrics", + "freebayes" ], "update_time": "2019-03-04", "versions": 0 @@ -131734,9 +147006,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d10d692b30b89cca", @@ -131759,15 +147031,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "db8443163482a2e0", @@ -131780,20 +147052,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "vcfselectsamples", + "sort1", + "freebayes", + "snpEff", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "snpEff", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "vcfselectsamples", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2019-02-15", "versions": 1 @@ -131816,8 +147088,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "peakcalling_macs", - "bowtie2" + "bowtie2", + "peakcalling_macs" ], "update_time": "2019-02-15", "versions": 1 @@ -131838,14 +147110,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2019-02-11", "versions": 4 @@ -131866,13 +147138,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", "CONVERTER_interval_to_bed_0", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2019-02-11", "versions": 0 @@ -131882,10 +147154,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence alignment", "Sequence composition calculation", - "Statistical calculation" + "Statistical calculation", + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "6c49d9c25ba4ddf5", @@ -131898,12 +147170,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "trimmomatic", "cshl_fastq_quality_filter", - "hisat2", "cufflinks", - "fastqc" + "trimmomatic", + "fastqc", + "hisat2", + "samtools_flagstat" ], "update_time": "2019-02-11", "versions": 11 @@ -131914,11 +147186,11 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", - "Multiple sequence alignment", "Sequence analysis", + "Sequence alignment", + "Global alignment", "Local alignment", - "Sequence alignment" + "Multiple sequence alignment" ], "edam_topic": [], "id": "8d8e8927d63803ef", @@ -131931,12 +147203,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta2tab", + "rbc_mafft", "collapse_dataset", "tab2fasta", - "rbc_mafft", - "EMBOSS: extractseq35", - "tp_cat" + "fasta2tab", + "tp_cat", + "EMBOSS: extractseq35" ], "update_time": "2019-02-10", "versions": 3 @@ -131946,17 +147218,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "3565de0b5f5da36f", @@ -131969,19 +147241,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "Filter1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2019-02-06", "versions": 1 @@ -132012,10 +147284,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Sequencing quality control", - "Statistical calculation", - "Sequence composition calculation" + "Sequence composition calculation", + "Read mapping", + "Statistical calculation" ], "edam_topic": [], "id": "e6b48a02789d1879", @@ -132028,11 +147300,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", "naive_variant_caller", - "trimmomatic", "samtool_filter2", - "fastqc", - "bowtie2" + "trimmomatic", + "fastqc" ], "update_time": "2019-01-10", "versions": 0 @@ -132065,12 +147337,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "36bd1c3d32150b90", @@ -132083,17 +147355,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "trimmomatic", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", "picard_SortSam", "fastqc", - "bedtools_coveragebed", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2019-01-03", "versions": 2 @@ -132103,11 +147375,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Primer removal", "Read pre-processing", + "Sequence alignment", "Sequence trimming", - "Sequence alignment" + "Primer removal", + "Data handling" ], "edam_topic": [], "id": "5fc0c7c65edc7457", @@ -132121,8 +147393,8 @@ "tags": [], "tools": [ "rna_star", - "trim_galore", - "fastq_dump" + "fastq_dump", + "trim_galore" ], "update_time": "2019-01-02", "versions": 11 @@ -132132,9 +147404,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -132148,12 +147420,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", "sam_to_fastq", - "sam_to_bam", + "bam_to_sam", "Grep1", - "bam_to_sam" + "sam_to_bam", + "bwa_mem", + "samtools_flagstat" ], "update_time": "2018-12-07", "versions": 0 @@ -132163,9 +147435,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -132201,10 +147473,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", "cuffdiff", "cuffmerge", - "tophat2", - "cufflinks" + "tophat2" ], "update_time": "2018-12-04", "versions": 6 @@ -132214,11 +147486,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Formatting", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "ba5ea0a943d4359d", @@ -132231,16 +147503,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gatk_variant_filtration", "gatk_table_recalibration", - "bwa_mem", - "picard_MarkDuplicates", "trimmomatic", - "gatk_variant_select", "gatk_count_covariates", "samtools_sort", - "gatk_variant_filtration", + "gatk_variant_select", "gatk_analyze_covariates", - "gatk_unified_genotyper" + "gatk_unified_genotyper", + "bwa_mem", + "picard_MarkDuplicates" ], "update_time": "2018-11-30", "versions": 15 @@ -132261,11 +147533,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2018-11-13", "versions": 1 @@ -132290,12 +147562,12 @@ ], "tools": [ "Add_a_column1", - "Grep1", - "Cut1", "bed2gff1", - "addValue", + "Grep1", "Remove beginning1", - "tp_replace_in_column" + "tp_replace_in_column", + "Cut1", + "addValue" ], "update_time": "2018-11-13", "versions": 3 @@ -132316,11 +147588,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2018-11-08", "versions": 2 @@ -132367,12 +147639,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2018-11-08", "versions": 0 @@ -132382,10 +147654,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "27327a985fa9147f", @@ -132410,17 +147682,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Sequence file editing", "Statistical calculation", "Genome assembly", + "Sequence alignment", + "Sequencing quality control", + "Sequence file editing", + "Aggregation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "69514a75e4c9af08", @@ -132433,12 +147705,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", "naive_variant_caller", - "bwa", "seqtk_trimfq", + "unicycler", + "bwa_mem", "fastqc", - "unicycler" + "bwa" ], "update_time": "2018-10-25", "versions": 1 @@ -132481,16 +147753,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", "sam_bw_filter", - "gatk_realigner_target_creator", - "sam_pileup", - "varscan", "gatk_indel_realigner", + "varscan", "rgPicardMarkDups", - "vcfcombine", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "sam_pileup", + "picard_ARRG", + "gatk_realigner_target_creator", + "vcfcombine" ], "update_time": "2018-10-16", "versions": 2 @@ -132512,14 +147784,14 @@ "tags": [], "tools": [ "cat1", + "sort1", "sam_bw_filter", - "fastq_groomer", - "gatk_realigner_target_creator", "gatk_indel_realigner", - "sort1", - "bwa_wrapper", + "Grep1", "gatk_unified_genotyper", - "Grep1" + "bwa_wrapper", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2018-10-08", "versions": 0 @@ -132540,17 +147812,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta2tab", "fastq_paired_end_joiner", - "tp_awk_tool", - "Cut1", - "tp_find_and_replace", + "fastq_to_fasta_python", "tab2fasta", + "tp_find_and_replace", + "cshl_fastx_collapser", + "fasta2tab", + "Convert characters1", "trimmer", + "Cut1", "addValue", - "Convert characters1", - "cshl_fastx_collapser", - "fastq_to_fasta_python" + "tp_awk_tool" ], "update_time": "2018-09-11", "versions": 1 @@ -132560,17 +147832,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "62b052f47ccf0a8c", @@ -132585,18 +147857,18 @@ "polymorphism" ], "tools": [ - "bwa_mem", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2018-09-04", "versions": 0 @@ -132607,12 +147879,12 @@ "doi": "", "edam_operation": [ "Peak calling", + "Sequence composition calculation", "Gene regulatory network analysis", "Statistical calculation", - "Sequence composition calculation", + "Sequencing quality control", "Read mapping", - "Enrichment analysis", - "Sequencing quality control" + "Enrichment analysis" ], "edam_topic": [], "id": "4a95226c24ccbf3c", @@ -132625,18 +147897,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_plot_heatmap", + "deeptools_plot_correlation", + "bowtie2", + "macs2_callpeak", "deeptools_multi_bam_summary", + "samtools_idxstats", "trimmomatic", - "deeptools_plot_fingerprint", "samtools_sort", - "deeptools_plot_correlation", "deeptools_bam_compare", - "fastqc", + "deeptools_plot_fingerprint", + "deeptools_plot_heatmap", "deeptools_compute_matrix", - "macs2_callpeak", - "bowtie2", - "samtools_idxstats" + "fastqc" ], "update_time": "2018-08-16", "versions": 1 @@ -132647,12 +147919,12 @@ "doi": "", "edam_operation": [ "Peak calling", + "Sequence composition calculation", "Gene regulatory network analysis", "Statistical calculation", - "Sequence composition calculation", + "Sequencing quality control", "Read mapping", - "Enrichment analysis", - "Sequencing quality control" + "Enrichment analysis" ], "edam_topic": [], "id": "57fdd0bae83f2c97", @@ -132665,18 +147937,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_plot_heatmap", + "deeptools_plot_correlation", + "bowtie2", + "macs2_callpeak", "deeptools_multi_bam_summary", + "samtools_idxstats", "trimmomatic", - "deeptools_plot_fingerprint", "samtools_sort", - "deeptools_plot_correlation", "deeptools_bam_compare", - "fastqc", + "deeptools_plot_fingerprint", + "deeptools_plot_heatmap", "deeptools_compute_matrix", - "macs2_callpeak", - "bowtie2", - "samtools_idxstats" + "fastqc" ], "update_time": "2018-08-16", "versions": 5 @@ -132686,14 +147958,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "Primer removal", "Sequencing quality control", - "Formatting", - "Read mapping" + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "bb9e69ae66c3d916", @@ -132706,11 +147978,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "cufflinks", "trim_galore", "picard_SortSam", - "cufflinks", - "fastqc", - "bowtie2" + "fastqc" ], "update_time": "2018-08-16", "versions": 2 @@ -132720,11 +147992,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "Primer removal", "Sequencing quality control", "Read mapping" ], @@ -132739,11 +148011,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trim_galore", - "samtools_sort", + "bowtie2", "cufflinks", - "fastqc", - "bowtie2" + "samtools_sort", + "trim_galore", + "fastqc" ], "update_time": "2018-08-16", "versions": 1 @@ -132764,12 +148036,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "sort1", "Add_a_column1", + "Filter1", "Count1", - "Cut1", - "sort1", "XY_Plot_1", - "Filter1" + "Cut1" ], "update_time": "2018-08-15", "versions": 17 @@ -132793,14 +148065,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2018-08-14", "versions": 3 @@ -132810,13 +148082,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "a383ce2e2bc3c7b9", @@ -132830,11 +148102,11 @@ "tags": [], "tools": [ "mothur_screen_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", "mothur_summary_seqs", + "mothur_align_seqs", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_count_seqs", + "mothur_unique_seqs" ], "update_time": "2018-08-08", "versions": 1 @@ -132844,11 +148116,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Genome assembly", - "Sequencing quality control" + "Sequencing quality control", + "Aggregation" ], "edam_topic": [], "id": "db0671862a57968d", @@ -132884,10 +148156,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", "cuffdiff", "cuffmerge", - "tophat2", - "cufflinks" + "tophat2" ], "update_time": "2018-08-01", "versions": 0 @@ -132910,8 +148182,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "hisat2", "cshl_fasta_nucleotides_changer", + "hisat2", "cshl_fastx_collapser" ], "update_time": "2018-07-31", @@ -132922,12 +148194,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Statistical calculation", + "Sequence alignment", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "cbfdd5c8261fea57", @@ -132940,11 +148212,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "bamleftalign", - "naive_variant_caller", "allele_counts_1", - "Filter1" + "naive_variant_caller", + "Filter1", + "bwa_mem", + "bamleftalign" ], "update_time": "2018-07-24", "versions": 6 @@ -132965,10 +148237,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sequence_content_trimmer", - "make_families", "align_families", "correct_barcodes", + "sequence_content_trimmer", + "make_families", "dunovo" ], "update_time": "2018-07-22", @@ -132979,16 +148251,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "10d8d47f97afc999", @@ -133002,20 +148274,20 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "freebayes", "trimmomatic", - "vcffilter2", + "samtools_idxstats", + "sort1", "table_annovar", + "vcffilter2", + "bam_to_sam", "Summary_Statistics1", - "freebayes", - "samtool_filter2", - "sort1", + "bwa_mem", "fastqc", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-06-29", "versions": 0 @@ -133025,15 +148297,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Formatting", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Formatting", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "38cc6577c9b15275", @@ -133046,18 +148318,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "tp_sort_header_tool", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", - "Grouping1", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "Filter1", + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "tp_sort_header_tool", + "Grouping1", + "bwa_mem", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2018-06-25", "versions": 34 @@ -133067,9 +148339,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Read mapping", "Mapping", - "Data handling", - "Read mapping" + "Data handling" ], "edam_topic": [], "id": "73f5b1a6fd3c703f", @@ -133082,13 +148354,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gff2bed1", - "tp_sorted_uniq", + "bowtie2", "samtools_sort", - "rseqc_RPKM_saturation", + "Grep1", "bedtools_sortbed", - "bowtie2", - "Grep1" + "gff2bed1", + "tp_sorted_uniq", + "rseqc_RPKM_saturation" ], "update_time": "2018-06-06", "versions": 4 @@ -133098,13 +148370,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "64fa13bb48fcd7df", @@ -133117,20 +148389,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "mothur_pre_cluster", - "mothur_chimera_uchime", "mothur_screen_seqs", - "mothur_classify_seqs", + "mothur_pre_cluster", "mothur_remove_lineage", - "mothur_remove_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", "mothur_summary_seqs", - "mothur_seq_error", + "mothur_align_seqs", + "mothur_chimera_uchime", "mothur_get_groups", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_make_contigs", - "mothur_align_seqs" + "mothur_count_seqs", + "mothur_seq_error", + "mothur_unique_seqs", + "mothur_classify_seqs" ], "update_time": "2018-05-17", "versions": 1 @@ -133154,9 +148426,9 @@ "tags": [], "tools": [ "rna_star", + "cufflinks", "cuffdiff", - "cuffmerge", - "cufflinks" + "cuffmerge" ], "update_time": "2018-05-09", "versions": 0 @@ -133166,17 +148438,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "67e56a9919ed84f7", @@ -133190,19 +148462,19 @@ "tags": [], "tools": [ "cat1", - "bwa_mem", + "vcfselectsamples", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", - "vcfselectsamples", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2018-05-08", "versions": 0 @@ -133212,18 +148484,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", + "Sequence composition calculation", + "Sequence alignment analysis", + "Generation", "Genome indexing", - "Generation" + "Sequence trimming", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "2219c4aa7eb8cfb8", @@ -133236,14 +148508,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", - "samtools_flagstat", - "tp_sort_header_tool", "trimmomatic", - "bwa", + "deeptools_bam_coverage", "trim_galore", + "tp_sort_header_tool", "fastqc", - "bamFilter" + "bamFilter", + "bwa", + "samtools_flagstat" ], "update_time": "2018-05-07", "versions": 5 @@ -133266,10 +148538,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Grouping1", "tp_sort_header_tool", - "kraken", "kraken-translate", - "Grouping1" + "kraken" ], "update_time": "2018-04-10", "versions": 4 @@ -133298,17 +148570,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "86be1351ffb6498c", @@ -133321,19 +148593,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2018-04-09", "versions": 0 @@ -133343,16 +148615,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "c57c820557ae9b55", @@ -133366,22 +148638,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-04-08", "versions": 0 @@ -133391,9 +148663,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "3771c5db96f8f246", @@ -133406,16 +148678,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "samtools_mpileup", - "cuffmerge", - "cuffcompare", - "varscan", - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", + "bam_to_sam", + "varscan", + "cuffcompare", "fastqc", - "bam_to_sam" + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2018-04-08", "versions": 0 @@ -133425,16 +148697,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "cfd37af9d6e4cbdb", @@ -133448,21 +148720,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-04-04", "versions": 0 @@ -133472,16 +148744,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "d50b2df115706adb", @@ -133495,21 +148767,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "table_annovar", + "Filter1", "vcffilter2", + "bam_to_sam", + "tp_sort_header_tool", "Summary_Statistics1", - "table_annovar", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-04-04", "versions": 1 @@ -133519,16 +148791,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "5cad854edbbd3b69", @@ -133541,24 +148813,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_coveragebed", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "snpEff", "table_annovar", + "Filter1", + "tp_sort_header_tool", "vcf2tsv", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "snpSift_filter" + "snpSift_filter", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2018-04-03", "versions": 0 @@ -133568,16 +148840,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "4d251ecda59c87c5", @@ -133591,22 +148863,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-03-31", "versions": 0 @@ -133616,10 +148888,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence alignment", "Sequence composition calculation", - "Statistical calculation" + "Statistical calculation", + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "f47f0b25c1405128", @@ -133632,14 +148904,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "cufflinks", "trimmomatic", "cuffcompare", - "cuffdiff", - "hisat2", - "cufflinks", "fastqc", - "cuffmerge" + "hisat2", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2018-03-29", "versions": 4 @@ -133649,16 +148921,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "9d626a89800a96ca", @@ -133671,22 +148943,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_coveragebed", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "snpEff", "table_annovar", + "Filter1", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "snpSift_filter" + "snpSift_filter", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2018-03-28", "versions": 1 @@ -133696,16 +148968,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "e57d595b0cde1614", @@ -133718,22 +148990,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_coveragebed", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "tp_sort_header_tool", + "freebayes", + "snpEff", "table_annovar", + "Filter1", + "tp_sort_header_tool", "Summary_Statistics1", - "snpEff", - "freebayes", - "samtool_filter2", + "bwa_mem", "fastqc", - "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "snpSift_filter" + "snpSift_filter", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2018-03-26", "versions": 6 @@ -133743,16 +149015,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "6822f413a3b09cb4", @@ -133766,22 +149038,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-03-03", "versions": 1 @@ -133791,8 +149063,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence annotation" + "Sequence annotation", + "Data handling" ], "edam_topic": [], "id": "c8653e558a68eb68", @@ -133805,11 +149077,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", "gffread", - "fastq_dump", "tophat2", "samtools_sort", - "cufflinks" + "fastq_dump" ], "update_time": "2018-03-02", "versions": 1 @@ -133819,11 +149091,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", - "Formatting", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "4fcfea3a6691e18b", @@ -133843,12 +149115,12 @@ "filtersam" ], "tools": [ - "bwa_mem", - "picard_ValidateSamFile", - "picard_MarkDuplicates", "samtool_filter2", "picard_CleanSam", - "picard_FixMateInformation" + "picard_ValidateSamFile", + "bwa_mem", + "picard_FixMateInformation", + "picard_MarkDuplicates" ], "update_time": "2018-03-01", "versions": 4 @@ -133858,16 +149130,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "adf531bc12766c9b", @@ -133881,21 +149153,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-02-27", "versions": 0 @@ -133905,16 +149177,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "dbcf0fbf5329b3fb", @@ -133928,21 +149200,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2018-02-26", "versions": 0 @@ -133965,9 +149237,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bedtools_intersectbed", + "bedtools_sortbed", "bed_to_bigBed", - "bedtools_sortbed" + "bedtools_intersectbed" ], "update_time": "2018-02-25", "versions": 4 @@ -133977,9 +149249,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "50fb074833eb9836", @@ -133992,8 +149264,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2018-02-23", "versions": 1 @@ -134014,11 +149286,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gops_coverage_1", "CONVERTER_gff_to_bed_0", + "Filter1", "Add_a_column1", - "Summary_Statistics1", - "gops_coverage_1", - "Filter1" + "Summary_Statistics1" ], "update_time": "2018-02-20", "versions": 0 @@ -134028,15 +149300,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Variant calling", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "df6b9760e071b91b", @@ -134049,16 +149321,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", - "picard_MarkDuplicates", - "trimmomatic", - "bwa", + "bowtie2", "samtools_rmdup", - "freebayes", "samtool_filter2", + "freebayes", + "trimmomatic", + "bwa_mem", "fastqc", - "bowtie2" + "bwa", + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2018-02-20", "versions": 6 @@ -134079,11 +149351,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2018-02-19", "versions": 1 @@ -134093,12 +149365,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Formatting", - "Variant calling" + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "803215ef8142c069", @@ -134111,12 +149383,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_MarkDuplicates", + "bowtie2", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "freebayes", "fastqc", - "bowtie2" + "picard_MarkDuplicates" ], "update_time": "2018-02-16", "versions": 1 @@ -134126,17 +149398,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", - "Read summarisation", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "d8d005a019fe76f7", @@ -134149,13 +149421,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rna_star", - "trim_galore", - "fastq_dump", "featurecounts", "multiqc", + "trim_galore", + "genomespace_importer", "fastqc", - "genomespace_importer" + "rna_star", + "fastq_dump" ], "update_time": "2018-02-06", "versions": 2 @@ -134165,8 +149437,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -134180,9 +149452,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "freebayes", - "table_annovar", "bowtie2", + "table_annovar", + "freebayes", "vcffilter2" ], "update_time": "2018-02-02", @@ -134204,10 +149476,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "gops_join_1", "Cut1", - "Grouping1" + "Grouping1", + "join1" ], "update_time": "2017-12-17", "versions": 0 @@ -134228,12 +149500,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", + "Filter1", "Extract genomic DNA 1", - "comp1", "Convert characters1", - "Grouping1", - "cufflinks", - "Filter1" + "comp1", + "Grouping1" ], "update_time": "2017-12-11", "versions": 11 @@ -134270,12 +149542,12 @@ "doi": "", "edam_operation": [ "Peak calling", + "Sequence composition calculation", "Gene regulatory network analysis", "Statistical calculation", - "Sequence composition calculation", + "Sequencing quality control", "Read mapping", - "Enrichment analysis", - "Sequencing quality control" + "Enrichment analysis" ], "edam_topic": [], "id": "21b416bcf0b8c8cf", @@ -134288,12 +149560,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "macs2_callpeak", "fastq_groomer", - "samtools_flagstat", "trimmomatic", "fastqc", - "macs2_callpeak", - "bowtie2" + "samtools_flagstat" ], "update_time": "2017-12-01", "versions": 3 @@ -134314,11 +149586,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-12-01", "versions": 1 @@ -134339,11 +149611,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-11-30", "versions": 1 @@ -134364,12 +149636,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2017-11-15", "versions": 0 @@ -134390,11 +149662,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2017-11-09", "versions": 3 @@ -134415,11 +149687,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1" ], "update_time": "2017-11-09", "versions": 0 @@ -134440,11 +149712,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-11-09", "versions": 3 @@ -134454,9 +149726,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "3fbaa9ae67362495", @@ -134469,9 +149741,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "fastq_quality_trimmer", "tophat2", - "fastq_quality_trimmer" + "fastqc" ], "update_time": "2017-11-09", "versions": 1 @@ -134492,11 +149764,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-11-09", "versions": 1 @@ -134506,9 +149778,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", "Sequence alignment", - "Variant calling", - "Statistical calculation" + "Variant calling" ], "edam_topic": [], "id": "2d44e2b020bf94f8", @@ -134521,14 +149793,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "table_annovar", - "vcffilter2", + "Filter1", "freebayes", - "vcfcombine", "sort1", - "hisat2", + "table_annovar", + "vcffilter2", "Grouping1", - "Filter1" + "hisat2", + "vcfcombine" ], "update_time": "2017-10-29", "versions": 1 @@ -134538,17 +149810,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "68d05aae72fcd2c9", @@ -134561,19 +149833,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2017-10-13", "versions": 0 @@ -134583,15 +149855,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "ff137b61d4ef1b86", @@ -134604,20 +149876,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "samtools_mpileup", + "samtools_stats", "picard_CollectInsertSizeMetrics", - "fastq_groomer", - "samtools_flagstat", - "picard_MarkDuplicates", + "freebayes", + "vcftools_annotate", "trimmomatic", - "samtools_mpileup", "table_annovar", - "bwa", + "bam_to_sam", "varscan", - "freebayes", - "samtools_stats", "fastqc", - "vcftools_annotate", - "bam_to_sam" + "samtools_flagstat", + "bwa", + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2017-10-06", "versions": 10 @@ -134627,8 +149899,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "2d50de9b95ad0808", @@ -134641,8 +149913,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deseq2", - "Remove beginning1" + "Remove beginning1", + "deseq2" ], "update_time": "2017-09-28", "versions": 0 @@ -134652,8 +149924,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "36a92f1f6d2212a4", @@ -134666,10 +149938,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", + "collection_column_join", "tp_easyjoin_tool", "Cut1", - "collection_column_join", - "Filter1", "deseq2" ], "update_time": "2017-09-27", @@ -134691,8 +149963,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", - "tp_find_and_replace" + "tp_find_and_replace", + "Cut1" ], "update_time": "2017-09-27", "versions": 5 @@ -134702,13 +149974,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", "Nucleic acid sequence analysis", - "Sequencing quality control", "Sequence alignment", - "Differential gene expression analysis" + "Differential gene expression analysis", + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d8afd017905d6702", @@ -134721,15 +149993,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", + "cshl_fastq_quality_filter", + "htseq_count", + "Filter1", "cshl_fastx_clipper", "Cut1", - "htseq_count", - "cshl_fastq_quality_filter", - "hisat2", "collection_column_join", + "tp_easyjoin_tool", "fastqc", - "Filter1", + "hisat2", "deseq2" ], "update_time": "2017-09-27", @@ -134740,12 +150012,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", "Sequencing quality control", - "Sequence alignment" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a8ddab36010ed4c3", @@ -134758,11 +150030,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "trimmomatic", - "rna_star", "fastqc", - "deseq2" + "rna_star", + "deseq2", + "fastq_groomer" ], "update_time": "2017-09-18", "versions": 15 @@ -134783,12 +150055,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Cut1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1", + "Cut1" ], "update_time": "2017-09-14", "versions": 0 @@ -134798,8 +150070,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -134813,14 +150085,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "bowtie2", + "freebayes", + "snpEff", "trimmomatic", "snpEff_download", "vcffilter2", - "snpEff", - "freebayes", "Convert characters1", - "bowtie2" + "fastq_groomer" ], "update_time": "2017-09-08", "versions": 1 @@ -134830,8 +150102,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -134845,13 +150117,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "bowtie2", + "freebayes", + "snpEff", "trimmomatic", "snpEff_download", "vcffilter2", - "snpEff", - "freebayes", - "bowtie2" + "fastq_groomer" ], "update_time": "2017-09-08", "versions": 1 @@ -134861,18 +150133,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Enrichment analysis", + "Exonic splicing enhancer prediction", + "Gene expression analysis", "Differential gene expression analysis", "Sequence alignment", - "Gene expression analysis", - "RNA-Seq analysis", - "Read summarisation", "Primer removal", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Exonic splicing enhancer prediction", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Enrichment analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "82681bd5f059e39a", @@ -134885,18 +150157,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cummeRbund", + "cufflinks", "dexseq_count", - "cuffcompare", - "rna_star", - "trim_galore", "featurecounts", - "cuffdiff", - "cummerbund_to_cuffdiff", - "cufflinks", - "salmon", "deseq2", + "salmon", + "cuffcompare", + "trim_galore", "dexseq", + "cummerbund_to_cuffdiff", + "rna_star", + "cummeRbund", + "cuffdiff", "cuffmerge" ], "update_time": "2017-09-04", @@ -134907,9 +150179,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Enrichment analysis", "Peak calling", - "Gene regulatory network analysis" + "Gene regulatory network analysis", + "Enrichment analysis" ], "edam_topic": [], "id": "671ca26597d27579", @@ -134937,9 +150209,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -134957,8 +150229,8 @@ ], "tools": [ "deeptools_bam_coverage", - "samtool_filter2", - "bwa" + "bwa", + "samtool_filter2" ], "update_time": "2017-09-01", "versions": 1 @@ -134968,10 +150240,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence merging", "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequence merging" ], "edam_topic": [], "id": "9a1fb6ecff886358", @@ -134984,13 +150256,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "cshl_fastx_artifacts_filter", - "fastq_trimmer", "cshl_fastq_quality_filter", "iuc_pear", "fastqc", - "cshl_fastq_to_fasta" + "fastq_trimmer", + "cshl_fastq_to_fasta", + "fastq_groomer" ], "update_time": "2017-09-01", "versions": 13 @@ -135000,9 +150272,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Peak calling", "Gene regulatory network analysis", - "Enrichment analysis", - "Peak calling" + "Enrichment analysis" ], "edam_topic": [], "id": "a3945ef04698a1c5", @@ -135018,11 +150290,11 @@ "tutorial" ], "tools": [ + "deeptools_plot_correlation", + "macs2_callpeak", "deeptools_multi_bam_summary", "deeptools_plot_fingerprint", - "macs2_predictd", - "deeptools_plot_correlation", - "macs2_callpeak" + "macs2_predictd" ], "update_time": "2017-08-29", "versions": 3 @@ -135032,9 +150304,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -135052,8 +150324,8 @@ ], "tools": [ "deeptools_bam_coverage", - "samtool_filter2", - "bwa" + "bwa", + "samtool_filter2" ], "update_time": "2017-08-29", "versions": 4 @@ -135074,10 +150346,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Remove beginning1", "Convert characters1", + "mergeCols1", "Grouping1", - "mergeCols1" + "Remove beginning1" ], "update_time": "2017-08-24", "versions": 0 @@ -135100,9 +150372,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bedtools_getfastabed", "bedtools_bamtobed", - "bedtools_mergebed", - "bedtools_getfastabed" + "bedtools_mergebed" ], "update_time": "2017-08-14", "versions": 1 @@ -135113,8 +150385,8 @@ "doi": "", "edam_operation": [ "Read mapping", - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "aae5b6d9beb860ba", @@ -135129,12 +150401,12 @@ "easy" ], "tools": [ - "cuffdiff", - "tophat2", - "cufflinks", - "deseq2", "bowtie2", - "cuffmerge" + "cufflinks", + "tophat2", + "cuffmerge", + "cuffdiff", + "deseq2" ], "update_time": "2017-08-11", "versions": 8 @@ -135144,13 +150416,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", + "Statistical calculation", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control" ], "edam_topic": [], "id": "c24cfddfc88a97a3", @@ -135163,11 +150435,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_multijoin_tool", "featurecounts", "multiqc", - "hisat2", - "fastqc" + "tp_multijoin_tool", + "fastqc", + "hisat2" ], "update_time": "2017-07-23", "versions": 0 @@ -135200,17 +150472,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "46d035f814a9b4f8", @@ -135223,16 +150495,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", + "picard_AddOrReplaceReadGroups", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2017-07-04", "versions": 1 @@ -135242,13 +150514,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Formatting", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "4164a02a6bd70893", @@ -135261,12 +150533,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "sam_merge2", + "freebayes", "table_annovar", + "sam_merge2", + "picard_AddOrReplaceReadGroups", "vcffilter2", - "freebayes", - "picard_AddOrReplaceReadGroups" + "bwa_mem" ], "update_time": "2017-06-30", "versions": 1 @@ -135287,11 +150559,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "cuffdiff", - "tophat2", "cufflinks", - "cuffmerge" + "tophat2", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2017-06-28", "versions": 1 @@ -135301,13 +150573,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence annotation", - "Differential gene expression analysis", + "RNA-Seq analysis", "Sequence alignment", + "Differential gene expression analysis", + "RNA-Seq quantification", "Read summarisation", - "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence annotation", + "Transcriptome assembly" ], "edam_topic": [], "id": "4061e061f659449b", @@ -135320,18 +150592,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "deeptools_bam_coverage", - "gffcompare", + "Filter1", + "featurecounts", "trimmomatic", + "stringtie_merge", + "deeptools_bam_coverage", "Cut1", + "Convert characters1", "join1", - "stringtie_merge", - "featurecounts", - "Filter1", + "gffcompare", + "stringtie", "hisat2", - "Convert characters1", - "deseq2", - "stringtie" + "deseq2" ], "update_time": "2017-06-22", "versions": 8 @@ -135341,13 +150613,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Formatting", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "63e0dcf18794dbc1", @@ -135361,16 +150633,16 @@ "tags": [], "tools": [ "cat1", - "bwa_mem", - "fastq_groomer", - "tp_sort_header_tool", - "vcffilter2", - "table_annovar", + "vcfselectsamples", "freebayes", - "Grouping1", + "table_annovar", "picard_MergeSamFiles", - "vcfselectsamples", - "picard_AddOrReplaceReadGroups" + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "tp_sort_header_tool", + "Grouping1", + "bwa_mem", + "fastq_groomer" ], "update_time": "2017-06-04", "versions": 0 @@ -135380,12 +150652,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "fc09d17e0bce18f8", @@ -135398,12 +150670,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "trimmomatic", - "fastq_dump", + "bowtie_wrapper", "featurecounts", + "trimmomatic", "CONVERTER_bed_to_gff_0", "fastqc", - "bowtie_wrapper" + "fastq_dump" ], "update_time": "2017-05-31", "versions": 3 @@ -135424,19 +150696,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_easyjoin_tool", "cat1", + "Filter1", + "sort1", "table_annovar", - "Grep1", - "Cut1", - "tp_sorted_uniq", "tp_replace_in_line", - "sort1", - "addValue", + "tp_cat", + "Grep1", "Convert characters1", - "Filter1", + "tp_easyjoin_tool", "vcf2tsv", - "tp_cat" + "tp_sorted_uniq", + "Cut1", + "addValue" ], "update_time": "2017-05-31", "versions": 2 @@ -135457,18 +150729,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "datamash_transpose", - "tp_cut_tool", "wc_gnu", - "tp_sed_tool", + "tp_head_tool", + "tp_tail_tool", "tp_replace_in_line", - "addValue", "tp_cat", - "mergeCols1", - "tp_head_tool", + "tp_sed_tool", "tp_replace_in_column", - "Paste1", - "tp_tail_tool" + "tp_cut_tool", + "mergeCols1", + "addValue" ], "update_time": "2017-05-30", "versions": 18 @@ -135478,9 +150750,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "8b2c8c8ce121177d", @@ -135493,14 +150765,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bam_to_sam", - "tp_cut_tool", - "cuffdiff", + "cufflinks", + "Filter1", "tophat2", + "bam_to_sam", "cuffquant", - "cufflinks", "fastqc", - "Filter1", + "tp_cut_tool", + "cuffdiff", "cuffmerge" ], "update_time": "2017-05-26", @@ -135511,9 +150783,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Variant calling", "Read mapping", "Formatting", - "Variant calling", "Statistical calculation" ], "edam_topic": [], @@ -135527,12 +150799,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_MarkDuplicates", + "bowtie2", "fastq_paired_end_joiner", - "vcffilter2", - "snpEff", "freebayes", - "bowtie2" + "snpEff", + "vcffilter2", + "picard_MarkDuplicates" ], "update_time": "2017-05-24", "versions": 3 @@ -135553,11 +150825,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-05-18", "versions": 1 @@ -135568,9 +150840,9 @@ "doi": "", "edam_operation": [ "Statistical calculation", + "Variant calling", "Read mapping", - "Formatting", - "Variant calling" + "Formatting" ], "edam_topic": [], "id": "399b4543d26990f2", @@ -135583,15 +150855,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "vcffilter2", - "table_annovar", - "freebayes", + "bowtie2", "sort1", - "Grouping1", + "freebayes", + "table_annovar", "picard_MergeSamFiles", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "Grouping1", + "fastq_groomer" ], "update_time": "2017-05-06", "versions": 1 @@ -135643,14 +150915,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "414fa13b613b33d8", @@ -135663,17 +150935,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", - "tp_sort_header_tool", - "vcffilter2", - "table_annovar", - "snpEff", "freebayes", - "Grouping1", + "snpEff", "Show beginning1", + "table_annovar", + "vcffilter2", + "tp_cat", + "tp_sort_header_tool", + "Grouping1", + "bwa_mem", "fastqc", - "tp_cat" + "fastq_groomer" ], "update_time": "2017-05-03", "versions": 0 @@ -135683,8 +150955,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "2478426a119d9d93", @@ -135697,11 +150969,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "vcfleftalign", "freebayes", - "vcfcombine", "samtool_filter2", - "bwa_wrapper" + "vcfleftalign", + "bwa_wrapper", + "vcfcombine" ], "update_time": "2017-04-09", "versions": 1 @@ -135711,17 +150983,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "20fe561687df596c", @@ -135734,19 +151006,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2017-04-08", "versions": 0 @@ -135756,9 +151028,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "6e6651ae846d8f83", @@ -135771,13 +151043,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "trimmomatic", "tophat2", + "gops_join_1", "comp1", "bwa_wrapper", "fastqc", - "gops_join_1" + "fastq_groomer" ], "update_time": "2017-04-07", "versions": 0 @@ -135787,16 +151059,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "bd184804cfddafc4", @@ -135810,21 +151082,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", "samtool_filter2", + "samtools_idxstats", + "trimmomatic", + "bedtools_coveragebed", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2017-04-03", "versions": 0 @@ -135834,17 +151106,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "9d456396b9cd79d7", @@ -135857,19 +151129,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2017-03-30", "versions": 0 @@ -135879,16 +151151,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "2644a8c0da3066c5", @@ -135902,22 +151174,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2017-03-29", "versions": 0 @@ -135927,16 +151199,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "61d03396ad7f25b9", @@ -135950,21 +151222,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2017-03-29", "versions": 0 @@ -135974,16 +151246,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "f60818a405f1bbbd", @@ -135997,22 +151269,22 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", - "snpEff", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", + "snpEff", + "vcffilter2", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2017-03-22", "versions": 0 @@ -136022,16 +151294,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "ef44d02a79bd28bf", @@ -136045,21 +151317,21 @@ "tags": [], "tools": [ "picard_CollectInsertSizeMetrics", - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", + "bedtools_coveragebed", + "samtool_filter2", + "samtools_idxstats", "trimmomatic", - "vcffilter2", - "table_annovar", - "Summary_Statistics1", "freebayes", - "samtool_filter2", "sort1", - "fastqc", + "table_annovar", "Filter1", - "bedtools_coveragebed", - "samtools_idxstats", - "bam_to_sam" + "vcffilter2", + "bam_to_sam", + "Summary_Statistics1", + "bwa_mem", + "fastqc", + "samtools_flagstat", + "picard_MarkDuplicates" ], "update_time": "2017-03-08", "versions": 0 @@ -136069,11 +151341,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -136087,12 +151359,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "samtools_mpileup", "trim_galore", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "fastq_groomer" ], "update_time": "2017-02-28", "versions": 1 @@ -136113,11 +151385,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-02-27", "versions": 1 @@ -136127,17 +151399,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "1d748868e78275dd", @@ -136150,19 +151422,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "Filter1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2017-02-11", "versions": 0 @@ -136183,11 +151455,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-02-11", "versions": 1 @@ -136208,11 +151480,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-02-10", "versions": 2 @@ -136254,11 +151526,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-02-10", "versions": 1 @@ -136279,11 +151551,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2017-02-09", "versions": 1 @@ -136325,10 +151597,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "snpEff", - "check_snpeff_candidates", "snpSift_filter", - "gatk_variant_select" + "gatk_variant_select", + "snpEff", + "check_snpeff_candidates" ], "update_time": "2017-01-16", "versions": 2 @@ -136349,14 +151621,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fasta2tab", - "Cut1", - "tab2fasta", "sort1", - "addValue", - "cshl_fasta_formatter", + "tab2fasta", "mergeCols1", "fasta_concatenate0", + "fasta2tab", + "cshl_fasta_formatter", + "Cut1", + "addValue", "fasta_compute_length" ], "update_time": "2017-01-12", @@ -136378,22 +151650,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", - "fastq_groomer", - "gatk_realigner_target_creator", + "fastq_stats", "gatk_indel_realigner", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2017-01-12", "versions": 2 @@ -136414,15 +151686,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", - "comp1", - "addValue", - "Remove beginning1", - "Convert characters1", + "Paste1", "Show beginning1", "mergeCols1", - "Paste1", - "tp_cat" + "tp_cat", + "Convert characters1", + "Remove beginning1", + "comp1", + "Cut1", + "addValue" ], "update_time": "2017-01-11", "versions": 11 @@ -136443,25 +151715,25 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "fastq_groomer", - "gatk_variant_select", + "gatk_depth_of_coverage", + "bwa_wrapper", + "sam_to_bam", + "Filter1", + "gatk_indel_realigner", + "gatk_unified_genotyper", "snp_mapping_using_wgs", + "picard_ARRG", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", "fastq_stats", + "rgPicardMarkDups", + "check_snpeff_candidates", "qual_stats_boxplot", - "gatk_unified_genotyper", - "sam_to_bam", + "gatk_variant_select", "snpSift_filter", "gatk_realigner_target_creator", - "check_snpeff_candidates", - "rgPicardMarkDups", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "sam_bw_filter", - "gatk_indel_realigner", - "bwa_wrapper", - "gatk_depth_of_coverage", - "Filter1" + "fastq_groomer" ], "update_time": "2017-01-10", "versions": 2 @@ -136485,12 +151757,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gatk_realigner_target_creator", + "bowtie2", "samtools_rmdup", "gatk_indel_realigner", + "picard_AddOrReplaceReadGroups", "gatk_unified_genotyper", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "gatk_realigner_target_creator" ], "update_time": "2017-01-09", "versions": 2 @@ -136500,11 +151772,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", - "Sequence analysis" + "Local alignment", + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "6b4ad51307a28c7f", @@ -136518,11 +151790,11 @@ "tags": [], "tools": [ "EMBOSS: freak36", + "EMBOSS: compseq14", "EMBOSS: cusp17", - "EMBOSS: newcpgseek58", "EMBOSS: cpgreport16", - "EMBOSS: infoseq46", - "EMBOSS: compseq14" + "EMBOSS: newcpgseek58", + "EMBOSS: infoseq46" ], "update_time": "2016-12-26", "versions": 1 @@ -136543,12 +151815,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tp_cut_tool", - "tp_awk_tool", - "Remove beginning1", - "Convert characters1", "Filter1", - "tp_replace_in_column" + "Convert characters1", + "Remove beginning1", + "tp_replace_in_column", + "tp_cut_tool", + "tp_awk_tool" ], "update_time": "2016-12-08", "versions": 7 @@ -136577,11 +151849,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -136595,10 +151867,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "samtools_stats", "trim_galore", - "tophat2" + "samtools_stats", + "tophat2", + "fastqc" ], "update_time": "2016-11-16", "versions": 6 @@ -136608,12 +151880,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "0cbab8b7044d24f9", @@ -136626,18 +151898,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "snpEff", + "trimmomatic", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", "picard_SortSam", "fastqc", - "bedtools_coveragebed", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2016-11-12", "versions": 0 @@ -136647,16 +151919,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "bd00c8a7a3b7e5be", @@ -136669,17 +151941,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", "samtool_filter2", - "picard_SortSam", + "snpEff", + "trimmomatic", "fastqc", - "bedtools_coveragebed" + "vcffilter2", + "picard_SortSam", + "bwa_mem", + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2016-11-11", "versions": 9 @@ -136689,12 +151961,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "840a7be198dc8ae4", @@ -136716,18 +151988,18 @@ "week8" ], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "snpEff", + "trimmomatic", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", "picard_SortSam", "fastqc", - "bedtools_coveragebed", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2016-11-11", "versions": 0 @@ -136737,12 +152009,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", "Formatting", - "Variant calling" + "Mapping" ], "edam_topic": [], "id": "05bf642dc7c58c40", @@ -136755,18 +152027,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", - "trimmomatic", - "vcffilter2", - "snpEff", + "bedtools_coveragebed", "freebayes", "samtool_filter2", + "snpEff", + "trimmomatic", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", "picard_SortSam", "fastqc", - "bedtools_coveragebed", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "samtools_flagstat" ], "update_time": "2016-11-10", "versions": 3 @@ -136790,11 +152062,11 @@ "snps" ], "tools": [ - "comp1", "sort1", - "Grouping1", "tp_head_tool", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2016-11-06", "versions": 1 @@ -136804,15 +152076,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "1e6a0d6395cf6221", @@ -136825,16 +152097,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "vcffilter2", - "table_annovar", + "sort1", "freebayes", "samtool_filter2", - "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", "Grouping1", - "fastqc", - "picard_CleanSam" + "bwa_mem", + "fastqc" ], "update_time": "2016-10-06", "versions": 1 @@ -136883,8 +152155,8 @@ "asbmr2016" ], "tools": [ - "join1", - "Cut1" + "Cut1", + "join1" ], "update_time": "2016-09-18", "versions": 4 @@ -136908,8 +152180,8 @@ ], "tools": [ "cat1", - "join1", - "Cut1" + "Cut1", + "join1" ], "update_time": "2016-09-18", "versions": 0 @@ -136935,8 +152207,8 @@ "asbmr2016" ], "tools": [ - "hisat2", - "htseq_count" + "htseq_count", + "hisat2" ], "update_time": "2016-09-17", "versions": 6 @@ -136960,8 +152232,8 @@ ], "tools": [ "sort1", - "Cut1", - "Filter1" + "Filter1", + "Cut1" ], "update_time": "2016-09-17", "versions": 4 @@ -136982,8 +152254,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sort1", "gops_join_1", + "sort1", "Grouping1" ], "update_time": "2016-09-15", @@ -136994,14 +152266,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", "Statistical calculation", - "Sequence composition calculation", - "Read mapping", - "Genome indexing", - "Generation", + "Sequence alignment", + "Sequencing quality control", "Formatting", - "Sequence alignment" + "Generation", + "Genome indexing", + "Sequence composition calculation", + "Read mapping" ], "edam_topic": [], "id": "3d5347f1e8ee7db2", @@ -137014,17 +152286,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "samtools_mpileup", "picard_CollectInsertSizeMetrics", - "bwa_mem", - "fastq_groomer", - "picard_MarkDuplicates", "trimmomatic", - "samtools_mpileup", "table_annovar", "varscan", - "picard_SortSam", + "vcf2tsv", + "bwa_mem", "fastqc", - "vcf2tsv" + "picard_SortSam", + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2016-08-26", "versions": 3 @@ -137034,9 +152306,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "fe2c0e4694c56b6b", @@ -137049,11 +152321,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", + "cufflinks", "trimmomatic", "tophat2", - "cufflinks", - "fastqc" + "fastqc", + "samtools_flagstat" ], "update_time": "2016-08-25", "versions": 0 @@ -137063,8 +152335,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -137078,10 +152350,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "freebayes", "bowtie2", - "vcfcombine", - "vcffilter2" + "freebayes", + "vcffilter2", + "vcfcombine" ], "update_time": "2016-08-07", "versions": 1 @@ -137091,17 +152363,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "62ae08ab1133c22f", @@ -137118,19 +152390,19 @@ "courseraproject" ], "tools": [ - "bwa_mem", - "fastq_groomer", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2016-07-31", "versions": 0 @@ -137140,17 +152412,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "df1fa0b73f741a9c", @@ -137163,19 +152435,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", + "picard_AddOrReplaceReadGroups", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2016-07-29", "versions": 0 @@ -137198,16 +152470,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tab2fasta", - "Cut1", "rbc_mafft", - "comp1", - "tp_grep_tool", "sort1", - "Grouping1", "Show beginning1", + "tab2fasta", + "tp_grep_tool", "gops_join_1", - "clustalw" + "comp1", + "Grouping1", + "clustalw", + "Cut1" ], "update_time": "2016-07-27", "versions": 0 @@ -137228,11 +152500,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gops_join_1", "tp_sort_header_tool", "Count1", - "join1", "comp1", - "gops_join_1" + "join1" ], "update_time": "2016-07-11", "versions": 0 @@ -137256,12 +152528,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gatk_realigner_target_creator", + "bowtie2", "samtools_rmdup", "gatk_indel_realigner", - "picard_SortSam", "gatk_unified_genotyper", - "bowtie2" + "picard_SortSam", + "gatk_realigner_target_creator" ], "update_time": "2016-06-30", "versions": 0 @@ -137271,9 +152543,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", "Nucleic acid sequence analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "dcf6f201b787d148", @@ -137298,11 +152570,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "RNA-Seq analysis", + "Statistical calculation", + "Transcriptome assembly", "Sequencing quality control", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5aa2caa2dcae1477", @@ -137315,15 +152587,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "cuffdiff", + "bowtie_wrapper", + "Filter1", "samtools_sort", "sam_to_bam", "fastqc", - "Filter1", "stringtie", - "bowtie_wrapper", - "cuffmerge" + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2016-06-26", "versions": 1 @@ -137333,9 +152605,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "091896754bcc8ec1", @@ -137348,11 +152620,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "fastq_filter", - "cshl_fastx_collapser", + "fastq_to_fasta_python", "fastqc", - "fastq_to_fasta_python" + "cshl_fastx_collapser", + "fastq_groomer" ], "update_time": "2016-06-17", "versions": 1 @@ -137363,12 +152635,12 @@ "doi": "", "edam_operation": [ "Peak calling", + "Sequence composition calculation", "Gene regulatory network analysis", "Statistical calculation", - "Sequence composition calculation", - "Mapping", + "Sequencing quality control", "Enrichment analysis", - "Sequencing quality control" + "Mapping" ], "edam_topic": [], "id": "07739fbbd53755f6", @@ -137381,20 +152653,20 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", + "bowtie_wrapper", + "macs2_callpeak", + "wig_to_bigWig", + "Filter1", "Add_a_column1", - "fastq_groomer", - "samtools_flagstat", - "bedtools_bamtobed", - "trimmomatic", - "Cut1", "histogram_rpy", - "Filter1", - "wig_to_bigWig", + "trimmomatic", + "sam_bw_filter", + "bedtools_bamtobed", "sam_to_bam", "fastqc", - "macs2_callpeak", - "bowtie_wrapper" + "samtools_flagstat", + "Cut1", + "fastq_groomer" ], "update_time": "2016-06-13", "versions": 6 @@ -137404,17 +152676,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Variant calling", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "9d2d8c39b63d8ef0", @@ -137427,18 +152699,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "bwa", - "freebayes", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "bwa", + "picard_MarkDuplicates" ], "update_time": "2016-06-11", "versions": 0 @@ -137459,13 +152731,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", "gd_find_intervals", - "Cut1", "gd_specify", + "gops_join_1", "gd_sum_gd_snp", - "Filter1", - "gops_join_1" + "Cut1" ], "update_time": "2016-06-09", "versions": 0 @@ -137508,11 +152780,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gd_average_fst", + "histogram_rpy", "gd_specify", - "gd_add_fst_column", "gd_filter_gd_snp", - "histogram_rpy" + "gd_add_fst_column", + "gd_average_fst" ], "update_time": "2016-06-09", "versions": 0 @@ -137522,15 +152794,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Formatting", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Formatting", + "Generation", "Genome indexing", - "Generation" + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "202648c6c615929b", @@ -137543,17 +152815,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "tp_sort_header_tool", - "vcffilter2", - "table_annovar", "freebayes", - "Grouping1", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "tp_sort_header_tool", + "Grouping1", + "bwa_mem", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2016-06-08", "versions": 0 @@ -137563,11 +152835,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Formatting", "Sequence alignment", + "Formatting", + "Generation", "Genome indexing", - "Generation" + "Read mapping" ], "edam_topic": [], "id": "5b2a0da883be03b7", @@ -137580,17 +152852,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "naive_variant_caller", - "sequence_content_trimmer", - "make_families", "allele_counts_1", - "bwa", + "naive_variant_caller", "align_families", "fastq_combiner", - "duplex", + "Filter1", "picard_MergeSamFiles", - "Filter1" + "duplex", + "make_families", + "sequence_content_trimmer", + "bwa_mem", + "bwa" ], "update_time": "2016-06-08", "versions": 2 @@ -137600,15 +152872,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "d3e656ab45f40c11", @@ -137621,13 +152893,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", - "table_annovar", "freebayes", - "vcfcombine", + "table_annovar", + "picard_AddOrReplaceReadGroups", + "bwa_mem", "fastqc", - "picard_AddOrReplaceReadGroups" + "vcfcombine", + "fastq_groomer" ], "update_time": "2016-06-05", "versions": 0 @@ -137638,8 +152910,8 @@ "doi": "", "edam_operation": [ "Multiple sequence alignment", - "Sequence motif recognition", "Sequence cluster visualisation", + "Sequence motif recognition", "Sequence visualisation" ], "edam_topic": [], @@ -137653,16 +152925,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Count1", - "tp_sorted_uniq", + "Filter1", "gd_new_oscar", "Remove beginning1", + "Count1", "Grouping1", "rgweblogo3", - "hgv_david", - "Filter1", "tp_replace_in_column", - "clustalw" + "clustalw", + "tp_sorted_uniq", + "hgv_david" ], "update_time": "2016-06-05", "versions": 14 @@ -137672,17 +152944,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "9b32025036bdacb9", @@ -137695,19 +152967,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", - "vcffilter2", - "table_annovar", + "Filter1", "freebayes", "sort1", + "picard_CleanSam", + "table_annovar", + "picard_MergeSamFiles", + "vcffilter2", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2016-06-05", "versions": 0 @@ -137717,15 +152989,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "ad6143e2f74e1e94", @@ -137738,19 +153010,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "vcfselectsamples", + "sort1", + "freebayes", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "tp_cat", "Grouping1", + "bwa_mem", "fastqc", - "vcfselectsamples", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2016-06-05", "versions": 0 @@ -137760,15 +153032,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "baab0758f2240225", @@ -137781,16 +153053,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", "vcffilter2", - "table_annovar", "tp_sort_header_tool", - "freebayes", "Grouping1", + "bwa_mem", "fastqc", - "picard_CleanSam" + "picard_MarkDuplicates" ], "update_time": "2016-06-05", "versions": 1 @@ -137800,11 +153072,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Variant calling" + "Read mapping" ], "edam_topic": [], "id": "df6c398b2d4f1e99", @@ -137817,19 +153089,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie2", + "vcfselectsamples", + "Filter1", + "freebayes", "cat1", - "fastq_groomer", + "sort1", "trimmomatic", "table_annovar", "vcfbreakcreatemulti", - "freebayes", - "sort1", + "Grep1", "Grouping1", "fastqc", - "Filter1", - "bowtie2", - "Grep1", - "vcfselectsamples" + "fastq_groomer" ], "update_time": "2016-06-04", "versions": 1 @@ -137839,8 +153111,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "1bd0d7ef0aca1363", @@ -137876,8 +153148,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_sort", - "htseq_count" + "htseq_count", + "samtools_sort" ], "update_time": "2016-06-03", "versions": 11 @@ -137887,9 +153159,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "97064f2af2f30dc4", @@ -137902,10 +153174,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "tophat2", "samtools_flagstat", - "trimmomatic" + "trimmomatic", + "tophat2", + "fastqc" ], "update_time": "2016-06-03", "versions": 1 @@ -137915,9 +153187,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "e4e5dec116e7240b", @@ -137930,11 +153202,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", + "cufflinks", "trimmomatic", "tophat2", - "cufflinks", - "fastqc" + "fastqc", + "samtools_flagstat" ], "update_time": "2016-06-03", "versions": 7 @@ -137972,14 +153244,14 @@ ], "tools": [ "gd_phylogenetic_tree", - "gd_population_structure", + "Filter1", "gd_prepare_population_structure", - "gd_pca", "gd_specify", - "gd_sum_gd_snp", - "gd_coverage_distributions", "gd_filter_gd_snp", - "Filter1" + "gd_pca", + "gd_coverage_distributions", + "gd_population_structure", + "gd_sum_gd_snp" ], "update_time": "2016-06-01", "versions": 0 @@ -137990,9 +153262,9 @@ "doi": "", "edam_operation": [ "Statistical calculation", + "Variant calling", "Read mapping", - "Formatting", - "Variant calling" + "Formatting" ], "edam_topic": [], "id": "729780617ceb80db", @@ -138005,15 +153277,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "vcffilter2", - "table_annovar", - "freebayes", + "bowtie2", "sort1", - "Grouping1", + "freebayes", + "table_annovar", "picard_MergeSamFiles", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "Grouping1", + "fastq_groomer" ], "update_time": "2016-05-31", "versions": 0 @@ -138037,9 +153309,9 @@ "tags": [], "tools": [ "Grep1", - "sam_to_bam", + "bwa_wrapper", "fastq_dump", - "bwa_wrapper" + "sam_to_bam" ], "update_time": "2016-05-31", "versions": 0 @@ -138049,9 +153321,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b18a41e364650fee", @@ -138065,10 +153337,10 @@ "tags": [], "tools": [ "cat1", - "fastq_groomer", - "cshl_fastx_reverse_complement", "trimmomatic", - "fastqc" + "fastqc", + "cshl_fastx_reverse_complement", + "fastq_groomer" ], "update_time": "2016-05-26", "versions": 34 @@ -138089,17 +153361,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", + "sort1", "Add_a_column1", - "tp_cut_tool", "Cut1", + "Convert characters1", + "comp1", "join1", + "tp_cut_tool", "tp_sorted_uniq", - "comp1", - "sort1", - "addValue", - "Convert characters1", "mergeCols1", - "Filter1" + "addValue" ], "update_time": "2016-05-25", "versions": 0 @@ -138109,10 +153381,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "d69ea491b99016f4", @@ -138125,15 +153397,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", - "fastq_groomer", - "picard_MarkDuplicates", + "cufflinks", "fastq_quality_trimmer", - "cuffdiff", + "cshl_fastx_clipper", "tophat2", - "cufflinks", "fastqc", - "cuffmerge" + "cuffdiff", + "picard_MarkDuplicates", + "cuffmerge", + "fastq_groomer" ], "update_time": "2016-05-25", "versions": 3 @@ -138154,17 +153426,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", + "sort1", "Add_a_column1", - "tp_cut_tool", "Cut1", + "Convert characters1", + "comp1", "join1", + "tp_cut_tool", "tp_sorted_uniq", - "comp1", - "sort1", - "addValue", - "Convert characters1", "mergeCols1", - "Filter1" + "addValue" ], "update_time": "2016-05-25", "versions": 0 @@ -138174,17 +153446,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "43ca7614f6bb03d2", @@ -138197,18 +153469,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2016-05-21", "versions": 0 @@ -138219,8 +153491,8 @@ "doi": "", "edam_operation": [ "Multiple sequence alignment", - "Sequence motif recognition", "Sequence cluster visualisation", + "Sequence motif recognition", "Sequence visualisation" ], "edam_topic": [], @@ -138234,11 +153506,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "rgweblogo3", "Filter1", "histogram_rpy", - "fasta_compute_length", - "clustalw" + "rgweblogo3", + "clustalw", + "fasta_compute_length" ], "update_time": "2016-05-19", "versions": 13 @@ -138248,8 +153520,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Variant calling", + "Read mapping", "Statistical calculation" ], "edam_topic": [], @@ -138263,8 +153535,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "freebayes", "bowtie2", + "freebayes", "vcffilter2" ], "update_time": "2016-05-15", @@ -138289,9 +153561,9 @@ "tags": [], "tools": [ "bowtie2", + "samtools_mpileup", "sam_to_bam", - "varscan", - "samtools_mpileup" + "varscan" ], "update_time": "2016-05-14", "versions": 1 @@ -138301,17 +153573,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "270e2cb6b02afc9c", @@ -138324,19 +153596,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2016-05-12", "versions": 0 @@ -138376,11 +153648,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2016-05-03", "versions": 1 @@ -138390,10 +153662,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "17a969fa9ac02cec", @@ -138406,19 +153678,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "gatk_table_recalibration", - "fastq_groomer", - "gatk_realigner_target_creator", - "vcffilter2", "picard_ReorderSam", + "gatk_table_recalibration", + "gatk_count_covariates", "gatk_indel_realigner", + "vcffilter2", "rgPicardMarkDups", - "gatk_count_covariates", - "bwa_wrapper", "gatk_unified_genotyper", + "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "picard_ARRG", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2016-04-28", "versions": 0 @@ -138428,15 +153700,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "865d2cc4d14ec7e1", @@ -138449,18 +153721,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", - "picard_MarkDuplicates", - "tp_sort_header_tool", - "vcffilter2", - "table_annovar", "freebayes", - "vcfcombine", + "fastqc", + "table_annovar", + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "tp_sort_header_tool", "Grouping1", "picard_SortSam", - "fastqc", - "picard_AddOrReplaceReadGroups" + "bwa_mem", + "picard_MarkDuplicates", + "vcfcombine", + "fastq_groomer" ], "update_time": "2016-04-27", "versions": 0 @@ -138481,12 +153753,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", - "join1", - "Cut1", - "Show beginning1", "Filter1", - "Paste1" + "Show beginning1", + "join1", + "Cut1" ], "update_time": "2016-04-23", "versions": 1 @@ -138496,9 +153768,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "14410527253c6f40", @@ -138511,11 +153783,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "sam_merge2", "tophat2", + "sam_merge2", + "fastqc", "fastq_trimmer", - "fastqc" + "fastq_groomer" ], "update_time": "2016-04-21", "versions": 1 @@ -138564,9 +153836,9 @@ ], "tools": [ "cshl_fastx_clipper", + "cshl_fastx_renamer", "fasta_filter_by_length", "cshl_fastx_trimmer", - "cshl_fastx_renamer", "cshl_fastx_collapser" ], "update_time": "2016-04-13", @@ -138639,14 +153911,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2016-04-12", "versions": 10 @@ -138675,12 +153947,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment analysis", "Sequencing quality control", - "Formatting" + "Formatting", + "Data handling" ], "edam_topic": [], "id": "1d1ee1fad4e20eeb", @@ -138694,13 +153966,13 @@ "tags": [], "tools": [ "naive_variant_caller", - "picard_MergeSamFiles", "fastq_quality_trimmer", + "picard_MergeSamFiles", + "picard_AddOrReplaceReadGroups", "bwa_wrapper", - "fastqc", - "bamFilter", "sam_to_bam", - "picard_AddOrReplaceReadGroups" + "fastqc", + "bamFilter" ], "update_time": "2016-04-07", "versions": 0 @@ -138721,8 +153993,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tophat2", - "cufflinks" + "cufflinks", + "tophat2" ], "update_time": "2016-04-03", "versions": 1 @@ -138756,10 +154028,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", "Sequencing quality control", - "Statistical calculation", - "Sequence composition calculation" + "Sequence composition calculation", + "Read mapping", + "Statistical calculation" ], "edam_topic": [], "id": "98c2e50add031fce", @@ -138776,11 +154048,11 @@ "mapping" ], "tools": [ - "fastq_groomer", - "fastq_quality_trimmer", + "bowtie2", "samtools_rmdup", + "fastq_quality_trimmer", "fastqc", - "bowtie2" + "fastq_groomer" ], "update_time": "2016-03-29", "versions": 1 @@ -138801,8 +154073,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tophat2", - "cufflinks" + "cufflinks", + "tophat2" ], "update_time": "2016-03-21", "versions": 1 @@ -138823,10 +154095,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "gops_join_1", "Cut1", - "Grouping1" + "Grouping1", + "join1" ], "update_time": "2016-03-19", "versions": 1 @@ -138847,10 +154119,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cufflinks", "cuffdiff", "cuffmerge", - "tophat2", - "cufflinks" + "tophat2" ], "update_time": "2016-03-11", "versions": 0 @@ -138871,11 +154143,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2016-03-09", "versions": 1 @@ -138896,11 +154168,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2016-03-07", "versions": 1 @@ -138910,11 +154182,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Variant calling", "Sequencing quality control", - "Formatting", - "Variant calling" + "Formatting" ], "edam_topic": [], "id": "f39603063febba82", @@ -138927,19 +154199,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "gatk_table_recalibration", - "fastq_groomer", - "gatk_realigner_target_creator", - "vcffilter2", "picard_ReorderSam", + "gatk_table_recalibration", + "freebayes", + "gatk_count_covariates", "gatk_indel_realigner", + "vcffilter2", "rgPicardMarkDups", - "gatk_count_covariates", - "freebayes", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "picard_ARRG", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2016-02-17", "versions": 3 @@ -138949,10 +154221,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "59659e3a065c642c", @@ -138965,19 +154237,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "gatk_table_recalibration", - "fastq_groomer", - "gatk_realigner_target_creator", - "vcffilter2", "picard_ReorderSam", + "gatk_table_recalibration", + "gatk_count_covariates", "gatk_indel_realigner", + "vcffilter2", "rgPicardMarkDups", - "gatk_count_covariates", - "bwa_wrapper", "gatk_unified_genotyper", + "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "picard_ARRG", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2016-02-17", "versions": 6 @@ -139001,12 +154273,12 @@ "selex" ], "tools": [ + "sort1", "Add_a_column1", + "Filter1", "Count1", - "Cut1", - "sort1", "XY_Plot_1", - "Filter1" + "Cut1" ], "update_time": "2016-02-09", "versions": 10 @@ -139030,14 +154302,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2016-02-09", "versions": 24 @@ -139061,14 +154333,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2016-02-09", "versions": 3 @@ -139092,14 +154364,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2016-02-09", "versions": 2 @@ -139123,14 +154395,14 @@ "selex" ], "tools": [ + "Paste1", "cat1", - "fasta2tab", - "Cut1", "cshl_fastx_renamer", - "join1", + "fasta2tab", "Convert characters1", - "cshl_fastx_collapser", - "Paste1" + "join1", + "Cut1", + "cshl_fastx_collapser" ], "update_time": "2016-02-09", "versions": 4 @@ -139140,13 +154412,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Formatting", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "9b81d47a468d6f99", @@ -139159,14 +154431,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "picard_MarkDuplicates", + "freebayes", + "vcfbedintersect", "vcffilter2", + "bam_to_sam", "vcfvcfintersect", + "samtools_flagstat", "bwa", - "freebayes", - "vcfbedintersect", - "bam_to_sam" + "picard_MarkDuplicates" ], "update_time": "2016-01-26", "versions": 8 @@ -139188,8 +154460,8 @@ "tags": [], "tools": [ "Count1", - "fasta2tab", - "fastq_to_fasta_python" + "fastq_to_fasta_python", + "fasta2tab" ], "update_time": "2016-01-25", "versions": 0 @@ -139212,13 +154484,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_merge2", - "samtools_flagstat", "picard_ReorderSam", - "cuffdiff", - "bedtools_genomecoveragebed_bedgraph", "wig_to_bigWig", - "tophat" + "bedtools_genomecoveragebed_bedgraph", + "sam_merge2", + "tophat", + "cuffdiff", + "samtools_flagstat" ], "update_time": "2016-01-23", "versions": -1 @@ -139229,10 +154501,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "d3a69b0b826331ef", @@ -139253,9 +154525,9 @@ "cat1", "tab2fasta", "Interval2Maf1", - "Convert characters1", + "EMBOSS: revseq82", "Grep1", - "EMBOSS: revseq82" + "Convert characters1" ], "update_time": "2016-01-07", "versions": 1 @@ -139266,9 +154538,9 @@ "doi": "", "edam_operation": [ "Statistical calculation", + "Variant calling", "Read mapping", - "Formatting", - "Variant calling" + "Formatting" ], "edam_topic": [], "id": "53f11afc67ffb66f", @@ -139281,15 +154553,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "vcffilter2", - "table_annovar", - "freebayes", + "bowtie2", "sort1", - "Grouping1", + "freebayes", + "table_annovar", "picard_MergeSamFiles", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "vcffilter2", + "picard_AddOrReplaceReadGroups", + "Grouping1", + "fastq_groomer" ], "update_time": "2015-12-22", "versions": 0 @@ -139321,8 +154593,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "535484d6482b80f4", @@ -139335,11 +154607,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "freebayes", "fastq_filter", + "freebayes", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "samtools_flagstat" ], "update_time": "2015-11-30", "versions": 7 @@ -139349,8 +154621,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -139364,15 +154636,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", + "random_lines1", "Draw_phylogram", - "tab2fasta", - "lca1", - "addValue", "trim_reads", - "random_lines1", - "Filter1" + "addValue" ], "update_time": "2015-11-29", "versions": 1 @@ -139393,11 +154665,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", "Add_a_column1", + "Extract genomic DNA 1", + "Convert characters1", "join1", - "Cut1", - "Convert characters1" + "Cut1" ], "update_time": "2015-11-18", "versions": 10 @@ -139418,10 +154690,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "PicardASMetrics", "bowtie_wrapper", + "fastq_stats", "sam_to_bam", - "fastq_stats" + "PicardASMetrics" ], "update_time": "2015-11-16", "versions": 1 @@ -139431,17 +154703,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "6d60c4491138813a", @@ -139457,19 +154729,19 @@ "calling" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "picard_MarkDuplicates", + "Filter1", + "sort1", + "freebayes", + "picard_CleanSam", "table_annovar", + "picard_MergeSamFiles", "vcffilter2", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", - "Filter1", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2015-11-12", "versions": 0 @@ -139479,8 +154751,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "1cd08f3549cf5589", @@ -139493,12 +154765,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "fastq_quality_trimmer", - "samtools_sort", "freebayes", + "samtools_sort", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "fastq_groomer" ], "update_time": "2015-11-10", "versions": 1 @@ -139519,11 +154791,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-11-06", "versions": 1 @@ -139546,11 +154818,11 @@ "kaffashow" ], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-10-28", "versions": 2 @@ -139560,17 +154832,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "e7030b62a3335bd7", @@ -139583,17 +154855,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "sort1", + "freebayes", + "table_annovar", "picard_MergeSamFiles", "vcffilter2", - "cshl_fastx_trimmer", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_AddOrReplaceReadGroups" + "cshl_fastx_trimmer" ], "update_time": "2015-10-23", "versions": 1 @@ -139625,9 +154897,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d89e626fa4f9434f", @@ -139640,11 +154912,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", - "fastq_groomer", "cshl_fastx_artifacts_filter", "fastq_quality_trimmer", - "fastqc" + "cshl_fastx_clipper", + "fastqc", + "fastq_groomer" ], "update_time": "2015-10-13", "versions": 2 @@ -139665,10 +154937,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "gops_join_1", "Cut1", - "Grouping1" + "Grouping1", + "join1" ], "update_time": "2015-10-09", "versions": 2 @@ -139689,11 +154961,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffmerge", - "cuffdiff", - "tophat2", "cufflinks", - "cuffcompare" + "tophat2", + "cuffcompare", + "cuffdiff", + "cuffmerge" ], "update_time": "2015-10-09", "versions": 0 @@ -139714,11 +154986,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffmerge", - "cuffdiff", - "tophat2", "cufflinks", - "cuffcompare" + "tophat2", + "cuffcompare", + "cuffdiff", + "cuffmerge" ], "update_time": "2015-10-09", "versions": 0 @@ -139739,11 +155011,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffmerge", - "cuffdiff", - "tophat2", "cufflinks", - "cuffcompare" + "tophat2", + "cuffcompare", + "cuffdiff", + "cuffmerge" ], "update_time": "2015-10-09", "versions": 0 @@ -139765,8 +155037,8 @@ "tags": [], "tools": [ "tab2fasta", - "fasta2tab", - "Grouping1" + "Grouping1", + "fasta2tab" ], "update_time": "2015-10-08", "versions": 8 @@ -139795,9 +155067,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Variant calling", "Read mapping", "Formatting", - "Variant calling", "Statistical calculation" ], "edam_topic": [], @@ -139811,14 +155083,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "bowtie2", + "sort1", + "freebayes", "table_annovar", "vcffilter2", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", - "bowtie2", - "picard_AddOrReplaceReadGroups" + "fastq_groomer" ], "update_time": "2015-09-30", "versions": 0 @@ -139828,17 +155100,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "7fb3396e45c5a33b", @@ -139851,19 +155123,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "sort1", + "freebayes", + "picard_CleanSam", + "table_annovar", "picard_MergeSamFiles", - "picard_MarkDuplicates", "vcffilter2", - "table_annovar", - "freebayes", - "sort1", + "picard_AddOrReplaceReadGroups", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates", + "fastq_groomer" ], "update_time": "2015-09-27", "versions": 0 @@ -139884,11 +155156,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-09-26", "versions": 1 @@ -139909,8 +155181,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "vcffilter2", - "samtools_mpileup" + "samtools_mpileup", + "vcffilter2" ], "update_time": "2015-09-25", "versions": 4 @@ -139931,10 +155203,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "gops_join_1", "Cut1", - "Grouping1" + "Grouping1", + "join1" ], "update_time": "2015-09-20", "versions": 0 @@ -139956,9 +155228,9 @@ "tags": [], "tools": [ "samtools_mpileup", + "Filter1", "Grep1", "bwa_wrapper", - "Filter1", "sam_to_bam" ], "update_time": "2015-08-30", @@ -139969,9 +155241,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "24adb067c82862fa", @@ -139985,9 +155257,9 @@ "tags": [], "tools": [ "fastqc", - "fastq_groomer", + "fastq_stats", "qual_stats_boxplot", - "fastq_stats" + "fastq_groomer" ], "update_time": "2015-08-30", "versions": 8 @@ -140008,12 +155280,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "fastq_groomer", - "samtools_flagstat", "samtools_rmdup", - "sam_to_bam", "peakcalling_macs", - "bowtie_wrapper" + "sam_to_bam", + "samtools_flagstat" ], "update_time": "2015-08-15", "versions": -1 @@ -140034,19 +155306,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tabular_to_fastq", - "Add_a_column1", - "fastq_groomer", - "Cut1", - "trimmer", - "comp1", + "Paste1", + "fastq_filter", "fastq_to_tabular", "sort1", - "fastq_filter", - "bwa_wrapper", "Filter1", "bowtie_wrapper", - "Paste1" + "Add_a_column1", + "comp1", + "bwa_wrapper", + "tabular_to_fastq", + "Cut1", + "trimmer", + "fastq_groomer" ], "update_time": "2015-07-30", "versions": 2 @@ -140056,12 +155328,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "483a98be358ce21c", @@ -140074,14 +155346,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", - "fastq_groomer", + "sort1", + "freebayes", "table_annovar", "vcffilter2", - "freebayes", - "sort1", "Convert characters1", - "Grouping1" + "Grouping1", + "bwa_mem", + "fastq_groomer" ], "update_time": "2015-07-26", "versions": 0 @@ -140102,11 +155374,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-07-18", "versions": 1 @@ -140116,12 +155388,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Statistical calculation", + "Sequence alignment", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "3767c9c07462b777", @@ -140134,18 +155406,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", - "bwa_mem", - "fastq_groomer", - "bamleftalign", - "fastq_quality_trimmer", + "cshl_fastx_quality_statistics", + "fastq_filter", + "bowtie2", "samtools_mpileup", + "fastq_quality_trimmer", + "cshl_fastx_clipper", "cshl_fastq_quality_converter", - "fastq_filter", + "cshl_fastq_quality_boxplot", "cshl_fastx_nucleotides_distribution", - "cshl_fastx_quality_statistics", - "bowtie2", - "cshl_fastq_quality_boxplot" + "bwa_mem", + "bamleftalign", + "fastq_groomer" ], "update_time": "2015-07-07", "versions": 1 @@ -140155,8 +155427,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "ada910fc3a68757a", @@ -140169,12 +155441,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "table_annovar", - "fastq_trimmer", "freebayes", + "table_annovar", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "fastq_trimmer", + "fastq_groomer" ], "update_time": "2015-07-04", "versions": 6 @@ -140206,13 +155478,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Read mapping", + "Generation", "Genome indexing", - "Sequencing quality control", + "Sequence composition calculation", + "Statistical calculation", "Sequence alignment", - "Generation" + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "f58970e6914a1bba", @@ -140225,10 +155497,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", "samtools_stats", + "fastq_groomer", "bwa_mem", - "fastq_groomer" + "fastqc" ], "update_time": "2015-06-20", "versions": 1 @@ -140238,9 +155510,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -140254,9 +155526,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bwa_mem", + "samtools_mpileup", "varscan", - "samtools_mpileup" + "bwa_mem" ], "update_time": "2015-06-20", "versions": 1 @@ -140266,9 +155538,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "48dd684196c65735", @@ -140281,11 +155553,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "cufflinks", "tophat2", + "fastqc", "fastq_trimmer", - "cufflinks", - "fastqc" + "fastq_groomer" ], "update_time": "2015-06-02", "versions": 0 @@ -140306,23 +155578,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", "snp_mapping_using_wgs", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2015-05-28", "versions": 2 @@ -140343,11 +155615,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-05-20", "versions": 1 @@ -140373,12 +155645,12 @@ "illumina" ], "tools": [ - "samtools_flagstat", - "samtools_rmdup", + "bowtie_wrapper", "wig_to_bigWig", - "sam_to_bam", "peakcalling_macs", - "bowtie_wrapper" + "samtools_rmdup", + "sam_to_bam", + "samtools_flagstat" ], "update_time": "2015-04-28", "versions": 8 @@ -140399,11 +155671,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-04-21", "versions": 1 @@ -140425,13 +155697,13 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "gops_subtract_1", - "Cut1", - "gops_merge_1", - "Filter1", "Grep1", - "gops_intersect_1" + "gops_intersect_1", + "gops_merge_1", + "Cut1" ], "update_time": "2015-04-19", "versions": 0 @@ -140452,11 +155724,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-04-15", "versions": 0 @@ -140477,11 +155749,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2015-04-11", "versions": 0 @@ -140526,22 +155798,22 @@ "tags": [], "tools": [ "cat1", - "Extract genomic DNA 1", - "picard_ARRG", - "gatk_realigner_target_creator", - "gatk_table_recalibration", "gatk_variant_combine", - "sam_pileup", - "gatk_variant_select", - "rgPicFixMate", + "sort1", "samtools_rmdup", - "gatk_indel_realigner", - "rgPicardMarkDups", + "gatk_table_recalibration", "gatk_count_covariates", - "sort1", + "gatk_indel_realigner", + "rgPicFixMate", + "gatk_variant_select", "gatk_analyze_covariates", + "rgPicardMarkDups", + "Extract genomic DNA 1", "gatk_unified_genotyper", - "sam_to_bam" + "sam_to_bam", + "sam_pileup", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2015-03-26", "versions": 0 @@ -140562,19 +155834,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tabular_to_fastq", - "Add_a_column1", - "fastq_groomer", - "Cut1", - "trimmer", - "comp1", + "Paste1", + "fastq_filter", "fastq_to_tabular", "sort1", - "fastq_filter", - "bwa_wrapper", "Filter1", "bowtie_wrapper", - "Paste1" + "Add_a_column1", + "comp1", + "bwa_wrapper", + "tabular_to_fastq", + "Cut1", + "trimmer", + "fastq_groomer" ], "update_time": "2015-03-23", "versions": 0 @@ -140595,19 +155867,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tabular_to_fastq", - "Add_a_column1", - "fastq_groomer", - "Cut1", - "trimmer", - "comp1", + "Paste1", + "fastq_filter", "fastq_to_tabular", "sort1", - "fastq_filter", - "bwa_wrapper", "Filter1", "bowtie_wrapper", - "Paste1" + "Add_a_column1", + "comp1", + "bwa_wrapper", + "tabular_to_fastq", + "Cut1", + "trimmer", + "fastq_groomer" ], "update_time": "2015-03-23", "versions": 0 @@ -140628,19 +155900,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "tabular_to_fastq", - "Add_a_column1", - "fastq_groomer", - "Cut1", - "trimmer", - "comp1", + "Paste1", + "fastq_filter", "fastq_to_tabular", "sort1", - "fastq_filter", - "bwa_wrapper", "Filter1", "bowtie_wrapper", - "Paste1" + "Add_a_column1", + "comp1", + "bwa_wrapper", + "tabular_to_fastq", + "Cut1", + "trimmer", + "fastq_groomer" ], "update_time": "2015-03-23", "versions": 2 @@ -140651,10 +155923,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "c92c9d046b394094", @@ -140667,13 +155939,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", "Add_a_column1", + "Extract genomic DNA 1", + "EMBOSS: fuzznuc37", "gff2bed1", + "Convert characters1", "Cut1", - "EMBOSS: fuzznuc37", - "addValue", - "Convert characters1" + "addValue" ], "update_time": "2015-03-22", "versions": -1 @@ -140697,10 +155969,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtool_filter2", "bowtie2", + "bedtools_bamtobed", "samtools_rmdup", - "bedtools_bamtobed" + "samtool_filter2" ], "update_time": "2015-03-17", "versions": 6 @@ -140710,10 +155982,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Variant calling" + "Statistical calculation", + "Variant calling", + "Sequencing quality control" ], "edam_topic": [], "id": "a23bf4cd3bc97f2a", @@ -140726,16 +155998,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "naive_variant_caller", - "sam_merge2", "allele_counts_1", + "naive_variant_caller", + "Filter1", "freebayes", + "sam_bw_filter", + "sam_merge2", "bwa_wrapper", + "sam_to_bam", "fastqc", - "Filter1", - "sam_to_bam" + "picard_ARRG" ], "update_time": "2015-03-06", "versions": 4 @@ -140778,14 +156050,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", + "sort1", "Add_a_column1", + "Show beginning1", + "Extract genomic DNA 1", + "gops_intersect_1", "Summary_Statistics1", - "Cut1", - "sort1", "Grouping1", - "Show beginning1", - "gops_intersect_1" + "Cut1" ], "update_time": "2015-02-19", "versions": 3 @@ -140795,9 +156067,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b4090679dcca6ce2", @@ -140812,9 +156084,9 @@ "rnaseq" ], "tools": [ - "fastqc", + "cufflinks", "tophat2", - "cufflinks" + "fastqc" ], "update_time": "2015-02-09", "versions": 3 @@ -140824,9 +156096,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "61d324b1eca6300e", @@ -140839,11 +156111,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", + "fastq_filter", "fastq_quality_trimmer", + "fastqc", "fastq_trimmer", - "fastq_filter", - "fastqc" + "fastq_groomer" ], "update_time": "2015-02-07", "versions": 1 @@ -140864,10 +156136,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "PicardASMetrics", - "rgEstLibComp", + "PicardGCBiasMetrics", "PicardInsertSize", - "PicardGCBiasMetrics" + "PicardASMetrics", + "rgEstLibComp" ], "update_time": "2015-01-26", "versions": 5 @@ -140888,12 +156160,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_BamIndexStats", - "PicardInsertSize", - "PicardGCBiasMetrics", "PicardASMetrics", + "gatk_depth_of_coverage", "rgEstLibComp", - "gatk_depth_of_coverage" + "PicardInsertSize", + "picard_BamIndexStats", + "PicardGCBiasMetrics" ], "update_time": "2015-01-26", "versions": 5 @@ -140903,9 +156175,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "3c32ad1a07a66843", @@ -140918,10 +156190,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "cshl_fastx_quality_statistics", "cshl_fastq_quality_boxplot", "cshl_fastx_nucleotides_distribution", - "cshl_fastx_quality_statistics" + "fastqc" ], "update_time": "2015-01-26", "versions": 9 @@ -140942,19 +156214,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", "gatk_table_recalibration", - "fastq_groomer", - "gatk_realigner_target_creator", - "gatk_variant_annotator", - "rgPicFixMate", - "gatk_indel_realigner", - "rgPicardMarkDups", + "sam_bw_filter", "gatk_count_covariates", + "gatk_indel_realigner", + "rgPicFixMate", + "gatk_variant_annotator", "gatk_analyze_covariates", - "bwa_wrapper", + "rgPicardMarkDups", "gatk_unified_genotyper", - "sam_to_bam" + "bwa_wrapper", + "sam_to_bam", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2015-01-26", "versions": 6 @@ -140975,10 +156247,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", - "sam_to_bam", "rgPicardMarkDups", - "samtools_mpileup" + "samtools_mpileup", + "sam_to_bam", + "sam_bw_filter" ], "update_time": "2015-01-26", "versions": 6 @@ -140999,19 +156271,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_table_recalibration", - "fastq_groomer", - "gatk_realigner_target_creator", "samtools_mpileup", - "rgPicFixMate", - "gatk_indel_realigner", - "rgPicardMarkDups", + "gatk_table_recalibration", + "sam_bw_filter", "gatk_count_covariates", + "gatk_indel_realigner", + "rgPicFixMate", "gatk_analyze_covariates", + "rgPicardMarkDups", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "picard_ARRG", + "gatk_realigner_target_creator", + "fastq_groomer" ], "update_time": "2015-01-26", "versions": 12 @@ -141042,9 +156314,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b7e20495b47d5b97", @@ -141057,12 +156329,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "cshl_fastx_nucleotides_distribution", "cshl_fastx_quality_statistics", + "cshl_fastq_quality_boxplot", "bwa_wrapper", + "cshl_fastx_nucleotides_distribution", "fastqc", - "cshl_fastq_quality_boxplot" + "fastq_groomer" ], "update_time": "2015-01-26", "versions": 21 @@ -141083,8 +156355,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "bwa_wrapper" + "bwa_wrapper", + "fastq_groomer" ], "update_time": "2015-01-26", "versions": 2 @@ -141105,16 +156377,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", "gatk_table_recalibration", - "gatk_realigner_target_creator", - "rgPicFixMate", - "gatk_indel_realigner", "gatk_count_covariates", - "rgPicardMarkDups", + "sam_bw_filter", + "gatk_indel_realigner", + "rgPicFixMate", "gatk_analyze_covariates", - "sam_to_bam" + "rgPicardMarkDups", + "sam_to_bam", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2015-01-26", "versions": 1 @@ -141146,9 +156418,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b0a12221ce09c001", @@ -141161,9 +156433,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "bowtie_wrapper", "cshl_fastx_clipper", - "bowtie_wrapper" + "fastqc" ], "update_time": "2015-01-15", "versions": 1 @@ -141184,9 +156456,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtool_filter2", "bowtie_wrapper", - "Grouping1" + "Grouping1", + "samtool_filter2" ], "update_time": "2014-12-09", "versions": 5 @@ -141196,9 +156468,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "e6838c861b6beaed", @@ -141211,9 +156483,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_trimmer", - "cshl_fastx_clipper", "fastqc", + "cshl_fastx_clipper", + "cshl_fastx_trimmer", "fastq_groomer" ], "update_time": "2014-12-04", @@ -141235,10 +156507,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "samtools_flagstat", - "samtools_rmdup", "bowtie_wrapper", - "sam_to_bam" + "samtools_rmdup", + "sam_to_bam", + "samtools_flagstat" ], "update_time": "2014-12-01", "versions": 0 @@ -141248,9 +156520,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "846b6fa2b8e20c3c", @@ -141263,9 +156535,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", + "cufflinks", "tophat2", - "cufflinks" + "fastqc" ], "update_time": "2014-11-25", "versions": 2 @@ -141286,9 +156558,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "peakcalling_macs", "bowtie_wrapper", - "fastq_stats" + "fastq_stats", + "peakcalling_macs" ], "update_time": "2014-11-25", "versions": 2 @@ -141310,8 +156582,8 @@ "tags": [], "tools": [ "gatk_unified_genotyper", - "sam_to_bam", - "bwa_wrapper" + "bwa_wrapper", + "sam_to_bam" ], "update_time": "2014-11-25", "versions": 0 @@ -141332,10 +156604,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bedtools_genomecoveragebed_histogram", "naive_variant_caller", - "fastq_groomer", - "bwa_wrapper" + "bwa_wrapper", + "bedtools_genomecoveragebed_histogram", + "fastq_groomer" ], "update_time": "2014-11-04", "versions": 0 @@ -141356,8 +156628,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sort1", "gops_join_1", + "sort1", "Grouping1" ], "update_time": "2014-10-26", @@ -141368,9 +156640,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "c3b3b2ee14bbd374", @@ -141383,16 +156655,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "fastq_groomer", "createInterval", - "rgPicardMarkDups", "gatk_depth_of_coverage", - "gatk_variant_eval", - "bwa_wrapper", + "rgPicardMarkDups", "gatk_unified_genotyper", + "bwa_wrapper", + "gatk_variant_eval", + "sam_to_bam", "fastqc", - "sam_to_bam" + "picard_ARRG", + "fastq_groomer" ], "update_time": "2014-10-22", "versions": 0 @@ -141402,9 +156674,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "eb20150175a6ab03", @@ -141417,13 +156689,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", - "fastq_groomer", + "bowtie_wrapper", "samtools_mpileup", - "fastq_trimmer", + "sam_bw_filter", "sam_to_bam", "fastqc", - "bowtie_wrapper" + "fastq_trimmer", + "fastq_groomer" ], "update_time": "2014-10-13", "versions": 1 @@ -141433,9 +156705,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "1b385fd45ee48614", @@ -141448,14 +156720,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", - "fastq_groomer", - "sam_pileup", + "bowtie_wrapper", "samtools_mpileup", - "fastq_trimmer", + "sam_bw_filter", "sam_to_bam", "fastqc", - "bowtie_wrapper" + "fastq_trimmer", + "sam_pileup", + "fastq_groomer" ], "update_time": "2014-10-13", "versions": 2 @@ -141477,8 +156749,8 @@ "tags": [], "tools": [ "gatk_unified_genotyper", - "sam_to_bam", - "bwa_wrapper" + "bwa_wrapper", + "sam_to_bam" ], "update_time": "2014-09-30", "versions": 1 @@ -141499,11 +156771,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2014-09-11", "versions": 3 @@ -141525,14 +156797,14 @@ "tags": [], "tools": [ "cat1", - "fastq_groomer", - "rgPicardMarkDups", "samtools_sort", - "LINKYX_Y", - "bwa_wrapper", "reformat_trinity_header", + "rgPicardMarkDups", + "bwa_wrapper", "sam_to_bam", - "trinityrnaseq" + "trinityrnaseq", + "LINKYX_Y", + "fastq_groomer" ], "update_time": "2014-09-10", "versions": 0 @@ -141553,15 +156825,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "samtools_sort", "LINKYX_mpileup", - "fastq_groomer", + "reformat_trinity_header", "rgPicardMarkDups", - "samtools_sort", - "LINKYX_X", "bwa_wrapper", - "reformat_trinity_header", "sam_to_bam", - "trinityrnaseq" + "trinityrnaseq", + "LINKYX_X", + "fastq_groomer" ], "update_time": "2014-09-10", "versions": 0 @@ -141586,10 +156858,10 @@ "formatting" ], "tools": [ - "tabular_to_fastq", - "join1", - "comp1", "fastq_to_tabular", + "comp1", + "join1", + "tabular_to_fastq", "addValue" ], "update_time": "2014-09-09", @@ -141622,9 +156894,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "4a5730954d776cb2", @@ -141637,21 +156909,21 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", "gatk_indel_realigner", - "rgPicardMarkDups", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", + "gatk_variant_select", "gatk_depth_of_coverage", - "bwa_wrapper", + "rgPicardMarkDups", "gatk_unified_genotyper", - "fastqc", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "fastqc", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2014-08-20", "versions": 0 @@ -141661,8 +156933,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -141682,17 +156954,17 @@ ], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2014-08-20", @@ -141750,10 +157022,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "b2176abeb937f026", @@ -141766,16 +157038,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", + "subtract_query1", "cshl_fastx_clipper", "sam_bw_filter", - "fastq_groomer", - "subtract_query1", - "cshl_fastx_trimmer", - "comp1", "picard_SamToFastq", + "comp1", "sam_to_bam", "fastqc", - "bowtie_wrapper" + "cshl_fastx_trimmer", + "fastq_groomer" ], "update_time": "2014-06-23", "versions": 3 @@ -141786,9 +157058,9 @@ "doi": "", "edam_operation": [ "Read mapping", - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "67c2ca24bc0be58e", @@ -141802,8 +157074,8 @@ "tags": [], "tools": [ "fastqc", - "fastq_groomer", - "bowtie2" + "bowtie2", + "fastq_groomer" ], "update_time": "2014-06-19", "versions": 1 @@ -141824,11 +157096,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "repeatmasker", "mgescan-nonltr", - "ltr-preprocessing-scaffold", + "find-ltr", "ltr-gff", - "repeatmasker", - "find-ltr" + "ltr-preprocessing-scaffold" ], "update_time": "2014-06-17", "versions": 0 @@ -141849,11 +157121,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gatk_realigner_target_creator", "gatk_indel_realigner", "rgPicardMarkDups", "gatk_unified_genotyper", - "bwa_wrapper" + "bwa_wrapper", + "gatk_realigner_target_creator" ], "update_time": "2014-06-15", "versions": 1 @@ -141874,8 +157146,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "snpEff", - "gatk_variant_select" + "gatk_variant_select", + "snpEff" ], "update_time": "2014-06-03", "versions": 3 @@ -141917,13 +157189,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gops_coverage_1", + "Filter1", "Add_a_column1", + "histogram_rpy", "Count1", - "gops_coverage_1", - "XY_Plot_1", "Grouping1", - "Filter1", - "histogram_rpy" + "XY_Plot_1" ], "update_time": "2014-05-13", "versions": 3 @@ -141944,9 +157216,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "gops_intersect_1", "Cut1", - "Add_a_column1", - "gops_intersect_1" + "Add_a_column1" ], "update_time": "2014-05-08", "versions": 3 @@ -141987,13 +157259,13 @@ "tags": [], "tools": [ "cat1", - "bedtools_genomecoveragebed_histogram", "Add_a_column1", - "XY_Plot_1", + "Show beginning1", + "Grep1", "Remove beginning1", "Grouping1", - "Show beginning1", - "Grep1" + "XY_Plot_1", + "bedtools_genomecoveragebed_histogram" ], "update_time": "2014-05-06", "versions": 0 @@ -142003,9 +157275,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "02d49c5f0d9aa010", @@ -142018,13 +157290,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "cshl_fastx_artifacts_filter", - "PicardASMetrics", "cshl_fastq_quality_filter", + "PicardASMetrics", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "fastq_groomer" ], "update_time": "2014-04-29", "versions": 1 @@ -142034,9 +157306,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "8356ee639055cbca", @@ -142049,14 +157321,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "cshl_fastx_artifacts_filter", - "fastq_trimmer", "cshl_fastq_quality_filter", "PicardASMetrics", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "fastq_trimmer", + "fastq_groomer" ], "update_time": "2014-04-29", "versions": 1 @@ -142110,9 +157382,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b9e3676a84b7be5d", @@ -142125,11 +157397,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "PicardASMetrics", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "fastq_groomer" ], "update_time": "2014-04-29", "versions": 7 @@ -142139,9 +157411,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "4703371e94b67347", @@ -142154,11 +157426,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", "PicardASMetrics", "bwa_wrapper", + "sam_to_bam", "fastqc", - "sam_to_bam" + "fastq_groomer" ], "update_time": "2014-04-29", "versions": 8 @@ -142179,8 +157451,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "flanking_features_1", - "Cut1" + "Cut1", + "flanking_features_1" ], "update_time": "2014-04-25", "versions": 2 @@ -142224,8 +157496,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gops_intersect_1", - "get_flanks1" + "get_flanks1", + "gops_intersect_1" ], "update_time": "2014-03-27", "versions": 2 @@ -142246,13 +157518,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", - "fastq_groomer", - "samtools_flagstat", + "bowtie_wrapper", "samtools_mpileup", + "fastq_groomer", + "pileup_interval", + "pileup_parser", "sam_to_bam", - "bowtie_wrapper", - "pileup_interval" + "samtools_flagstat" ], "update_time": "2014-03-25", "versions": 3 @@ -142273,9 +157545,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", "sort1", - "sam_to_bam" + "sam_to_bam", + "sam_bw_filter" ], "update_time": "2014-03-19", "versions": 0 @@ -142302,11 +157574,11 @@ "unique" ], "tools": [ + "sort1", + "Filter1", "sam_bw_filter", "comp1", - "sort1", - "Grouping1", - "Filter1" + "Grouping1" ], "update_time": "2014-03-19", "versions": 7 @@ -142332,15 +157604,15 @@ "workflow" ], "tools": [ - "samtools_flagstat", "samtools_mpileup", + "Filter1", "table_annovar", "varscan", "rgPicardMarkDups", "bwa_wrapper", + "sam_to_bam", "vcftools_annotate", - "Filter1", - "sam_to_bam" + "samtools_flagstat" ], "update_time": "2014-03-17", "versions": 0 @@ -142350,9 +157622,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "83fbcdf3e29c41d0", @@ -142367,23 +157639,23 @@ "variant-calling" ], "tools": [ - "picard_ARRG", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", "gatk_indel_realigner", - "rgPicardMarkDups", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "cloudmap_variant_discovery_mapping", + "gatk_variant_select", "gatk_depth_of_coverage", - "bwa_wrapper", + "rgPicardMarkDups", "gatk_unified_genotyper", - "fastqc", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "fastqc", + "snpSift_filter", + "cloudmap_variant_discovery_mapping", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2014-03-05", "versions": 0 @@ -142393,9 +157665,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "ea817818a6de77e0", @@ -142408,24 +157680,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", "snp_mapping_using_wgs", - "gatk_indel_realigner", - "rgPicardMarkDups", - "bedtools_genomecoveragebed_bedgraph", + "Filter1", "snpEff", - "cloudmap_variant_discovery_mapping", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", + "gatk_indel_realigner", + "gatk_variant_select", "gatk_depth_of_coverage", - "bwa_wrapper", + "rgPicardMarkDups", "gatk_unified_genotyper", - "fastqc", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "fastqc", + "snpSift_filter", + "cloudmap_variant_discovery_mapping", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2014-03-05", "versions": 0 @@ -142450,9 +157722,9 @@ ], "tools": [ "cuffcompare", + "cufflinks", "tophat", - "cuffmerge", - "cufflinks" + "cuffmerge" ], "update_time": "2014-02-23", "versions": 4 @@ -142473,8 +157745,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bcftools_view", - "samtools_mpileup" + "samtools_mpileup", + "bcftools_view" ], "update_time": "2014-02-18", "versions": 1 @@ -142497,9 +157769,9 @@ "tools": [ "cat1", "sort1", - "sam_to_bam", + "bam_to_sam", "Grep1", - "bam_to_sam" + "sam_to_bam" ], "update_time": "2014-02-18", "versions": 3 @@ -142531,10 +157803,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Database search", + "Sequencing quality control", "ID mapping" ], "edam_topic": [], @@ -142553,19 +157825,19 @@ "srnas" ], "tools": [ - "cshl_fastx_clipper", - "fastq_groomer", - "Fetch Taxonomic Ranks", "cshl_fastx_artifacts_filter", - "Count1", - "CONVERTER_sam_to_bam", - "Cut1", - "sort1", "fastq_filter", + "bowtie_wrapper", + "sort1", + "cshl_fastx_clipper", + "bam_to_sam", + "Fetch Taxonomic Ranks", "Convert characters1", + "CONVERTER_sam_to_bam", + "Count1", "fastqc", - "bowtie_wrapper", - "bam_to_sam" + "Cut1", + "fastq_groomer" ], "update_time": "2014-02-04", "versions": 1 @@ -142575,11 +157847,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Database search", + "Sequencing quality control", + "Read mapping", "ID mapping" ], "edam_topic": [], @@ -142598,23 +157870,23 @@ "viroid" ], "tools": [ + "cshl_fastx_artifacts_filter", "cat1", + "fastq_filter", + "bowtie2", + "sort1", "cshl_fastx_clipper", - "fastq_groomer", + "CONVERTER_Bam_Bai_0", + "bam_to_sam", "Fetch Taxonomic Ranks", - "cshl_fastx_artifacts_filter", - "Count1", - "CONVERTER_sam_to_bam", - "Cut1", - "sort1", - "fastq_filter", - "Convert characters1", "sam2interval", - "CONVERTER_Bam_Bai_0", - "fastqc", - "bowtie2", "Grep1", - "bam_to_sam" + "Convert characters1", + "CONVERTER_sam_to_bam", + "Count1", + "fastqc", + "Cut1", + "fastq_groomer" ], "update_time": "2014-02-03", "versions": 0 @@ -142635,11 +157907,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2014-01-21", "versions": -1 @@ -142723,9 +157995,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Grep1", "cat1", - "sort1", - "Grep1" + "sort1" ], "update_time": "2013-12-06", "versions": -1 @@ -142735,9 +158007,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "035c28a247976f2c", @@ -142750,13 +158022,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "cuffdiff", - "sort1", "cufflinks", - "fastqc", + "sort1", "tophat", - "cuffmerge" + "fastqc", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2013-11-19", "versions": 1 @@ -142829,9 +158101,9 @@ "human" ], "tools": [ - "join1", "Remove beginning1", - "Cut1" + "Cut1", + "join1" ], "update_time": "2013-10-14", "versions": 0 @@ -142852,10 +158124,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "CONVERTER_sam_to_bam", - "fastq_groomer", "samtools_flagstat", - "bwa_wrapper" + "fastq_groomer", + "bwa_wrapper", + "CONVERTER_sam_to_bam" ], "update_time": "2013-09-18", "versions": -1 @@ -142876,10 +158148,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "CONVERTER_sam_to_bam", - "fastq_groomer", "samtools_flagstat", - "bwa_wrapper" + "fastq_groomer", + "bwa_wrapper", + "CONVERTER_sam_to_bam" ], "update_time": "2013-09-18", "versions": 0 @@ -142903,10 +158175,10 @@ "macs" ], "tools": [ - "Cut1", - "Add_a_column1", + "Grep1", "Remove beginning1", - "Grep1" + "Cut1", + "Add_a_column1" ], "update_time": "2013-09-10", "versions": 0 @@ -142927,9 +158199,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Grep1", "cat1", - "sort1", - "Grep1" + "sort1" ], "update_time": "2013-08-12", "versions": -1 @@ -142996,10 +158268,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", - "addValue", "Convert characters1", - "mergeCols1" + "mergeCols1", + "addValue", + "Cut1" ], "update_time": "2013-07-30", "versions": 0 @@ -143027,13 +158299,13 @@ "cuffdiff" ], "tools": [ - "sam_merge2", - "samtools_flagstat", "picard_ReorderSam", - "cuffdiff", - "bedtools_genomecoveragebed_bedgraph", "wig_to_bigWig", - "tophat" + "bedtools_genomecoveragebed_bedgraph", + "sam_merge2", + "tophat", + "cuffdiff", + "samtools_flagstat" ], "update_time": "2013-07-23", "versions": 3 @@ -143054,11 +158326,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2013-07-19", "versions": 0 @@ -143081,13 +158353,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Count1", - "fastq_to_tabular", "cshl_fastq_quality_filter", + "fastq_to_tabular", "sort1", - "picard_SamToFastq", "Filter1", - "bam_to_sam" + "picard_SamToFastq", + "bam_to_sam", + "Count1" ], "update_time": "2013-07-17", "versions": 0 @@ -143115,13 +158387,13 @@ "cuffdiff" ], "tools": [ - "sam_merge2", - "samtools_flagstat", "picard_ReorderSam", - "cuffdiff", - "bedtools_genomecoveragebed_bedgraph", "wig_to_bigWig", - "tophat" + "bedtools_genomecoveragebed_bedgraph", + "sam_merge2", + "tophat", + "cuffdiff", + "samtools_flagstat" ], "update_time": "2013-07-17", "versions": 9 @@ -143143,12 +158415,12 @@ "tags": [], "tools": [ "cat1", - "Extract genomic DNA 1", + "Filter1", "Add_a_column1", + "Extract genomic DNA 1", + "gops_intersect_1", "Cut1", - "addValue", - "Filter1", - "gops_intersect_1" + "addValue" ], "update_time": "2013-07-09", "versions": -1 @@ -143170,13 +158442,13 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", + "gops_join_1", + "Grouping1", "join1", "Cut1", - "addValue", - "Grouping1", - "Filter1", - "gops_join_1" + "addValue" ], "update_time": "2013-07-04", "versions": 2 @@ -143198,10 +158470,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "Cut1", - "addValue", - "Filter1" + "addValue" ], "update_time": "2013-07-04", "versions": 1 @@ -143222,11 +158494,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "join1", - "addValue", "Grouping1", - "Filter1" + "join1", + "addValue" ], "update_time": "2013-07-04", "versions": 2 @@ -143248,10 +158520,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "Cut1", - "addValue", - "Filter1" + "addValue" ], "update_time": "2013-07-04", "versions": 2 @@ -143272,11 +158544,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "join1", - "addValue", "Grouping1", - "Filter1" + "join1", + "addValue" ], "update_time": "2013-07-04", "versions": 4 @@ -143298,10 +158570,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "Cut1", - "addValue", - "Filter1" + "addValue" ], "update_time": "2013-07-04", "versions": 2 @@ -143323,10 +158595,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "Cut1", - "addValue", - "Filter1" + "addValue" ], "update_time": "2013-07-04", "versions": 4 @@ -143347,11 +158619,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "join1", - "addValue", "Grouping1", - "Filter1" + "join1", + "addValue" ], "update_time": "2013-07-04", "versions": 3 @@ -143395,8 +158667,8 @@ "tags": [], "tools": [ "tophat", - "fastq_groomer", - "fastq_quality_trimmer" + "fastq_quality_trimmer", + "fastq_groomer" ], "update_time": "2013-06-13", "versions": 11 @@ -143406,9 +158678,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "cd14df23bb05db2c", @@ -143426,8 +158698,8 @@ "tools": [ "fastqc", "cshl_fastx_clipper", - "fastq_groomer", - "fastq_quality_trimmer" + "fastq_quality_trimmer", + "fastq_groomer" ], "update_time": "2013-06-03", "versions": 5 @@ -143437,9 +158709,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "f823b87dd06ba4ac", @@ -143452,14 +158724,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_merge2", - "samtools_flagstat", "bowtie_wrapper", - "fastq_paired_end_splitter", + "Filter1", + "histogram_rpy", + "sam_merge2", "sam_to_bam", "fastqc", - "Filter1", - "histogram_rpy" + "fastq_paired_end_splitter", + "samtools_flagstat" ], "update_time": "2013-05-28", "versions": 3 @@ -143469,9 +158741,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d2864aa3631b3bf6", @@ -143484,13 +158756,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_merge2", - "samtools_flagstat", "bowtie_wrapper", + "Filter1", + "histogram_rpy", + "sam_merge2", "sam_to_bam", "fastqc", - "Filter1", - "histogram_rpy" + "samtools_flagstat" ], "update_time": "2013-05-28", "versions": 1 @@ -143512,10 +158784,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", "Cut1", - "trimmer", - "Filter1" + "trimmer" ], "update_time": "2013-04-19", "versions": 13 @@ -143546,9 +158818,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "712d9ae42b45c4b9", @@ -143561,14 +158833,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "fastq_quality_trimmer", - "cuffmerge", - "cuffdiff", "cufflinks", - "fastqc", + "fastq_quality_trimmer", "tophat", - "cuffcompare" + "cuffcompare", + "fastqc", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2013-04-19", "versions": 0 @@ -143590,12 +158862,12 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", + "Grouping1", "join1", "Cut1", - "addValue", - "Grouping1", - "Filter1" + "addValue" ], "update_time": "2013-04-02", "versions": 3 @@ -143617,12 +158889,12 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Add_a_column1", + "Grouping1", "join1", "Cut1", - "addValue", - "Grouping1", - "Filter1" + "addValue" ], "update_time": "2013-04-02", "versions": -1 @@ -143643,11 +158915,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", - "fastq_groomer", + "bowtie_wrapper", "fastq_filter", + "cshl_fastx_clipper", "sam_to_bam", - "bowtie_wrapper" + "fastq_groomer" ], "update_time": "2013-03-20", "versions": -1 @@ -143657,9 +158929,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0599241ce8eae217", @@ -143672,10 +158944,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastqc", - "tophat", "fastq_groomer", - "cuffdiff" + "tophat", + "cuffdiff", + "fastqc" ], "update_time": "2013-03-18", "versions": 0 @@ -143685,9 +158957,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "77e4bb9d6aea0c9a", @@ -143701,10 +158973,10 @@ "tags": [], "tools": [ "cshl_fastx_clipper", - "fastq_groomer", - "cuffdiff", + "tophat", "fastqc", - "tophat" + "cuffdiff", + "fastq_groomer" ], "update_time": "2013-03-15", "versions": 0 @@ -143729,9 +159001,9 @@ "slop" ], "tools": [ - "gops_concat_1", + "get_flanks1", "gops_merge_1", - "get_flanks1" + "gops_concat_1" ], "update_time": "2013-03-15", "versions": 2 @@ -143755,10 +159027,10 @@ "cat1", "sam_bw_filter", "pileup_parser", - "sam_pileup", "Grep1", "bwa_wrapper", - "sam_to_bam" + "sam_to_bam", + "sam_pileup" ], "update_time": "2013-03-07", "versions": 0 @@ -143779,23 +159051,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", "snp_mapping_using_wgs", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2013-02-25", "versions": -1 @@ -143805,8 +159077,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -143821,17 +159093,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2013-02-16", @@ -143842,8 +159114,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -143858,17 +159130,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2013-02-11", @@ -143890,11 +159162,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "cshl_fastx_clipper", - "fastq_groomer", - "cuffdiff", "sam_to_bam", - "bowtie_wrapper" + "cuffdiff", + "fastq_groomer" ], "update_time": "2013-01-29", "versions": 1 @@ -143916,12 +159188,12 @@ "tags": [], "tools": [ "cat1", - "Add_a_column1", + "Filter1", "subtract_query1", - "Count1", + "Add_a_column1", "sam2interval", - "Filter1", - "Grep1" + "Grep1", + "Count1" ], "update_time": "2013-01-29", "versions": 2 @@ -143943,8 +159215,8 @@ "tags": [], "tools": [ "gops_join_1", - "Show beginning1", - "Grouping1" + "Grouping1", + "Show beginning1" ], "update_time": "2013-01-12", "versions": 0 @@ -143965,9 +159237,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "CONVERTER_bed_to_genetrack_0", "peakcalling_macs", - "build_ucsc_custom_track_1", - "CONVERTER_bed_to_genetrack_0" + "build_ucsc_custom_track_1" ], "update_time": "2012-12-19", "versions": 0 @@ -143977,9 +159249,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "462261c5e22635f0", @@ -143992,14 +159264,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "CONVERTER_bed_to_genetrack_0", - "cuffdiff", - "CONVERTER_interval_to_bedstrict_0", - "fastq_trimmer", "cufflinks", + "tophat", + "CONVERTER_interval_to_bedstrict_0", "CONVERTER_interval_to_bed6_0", "fastqc", - "tophat", + "fastq_trimmer", + "CONVERTER_bed_to_genetrack_0", + "cuffdiff", "cuffmerge" ], "update_time": "2012-12-17", @@ -144021,8 +159293,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", - "comp1" + "comp1", + "Filter1" ], "update_time": "2012-12-17", "versions": 2 @@ -144043,10 +159315,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bwa_wrapper", "peakcalling_macs", - "fastq_groomer", "sam_to_bam", - "bwa_wrapper" + "fastq_groomer" ], "update_time": "2012-12-12", "versions": 2 @@ -144069,8 +159341,8 @@ "tools": [ "tabular_to_fastq", "Filter1", - "tophat", - "fastq_manipulation" + "fastq_manipulation", + "tophat" ], "update_time": "2012-12-07", "versions": -1 @@ -144091,10 +159363,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Count1", - "sort1", "Paste1", - "mergeCols1" + "sort1", + "mergeCols1", + "Count1" ], "update_time": "2012-12-07", "versions": -1 @@ -144115,16 +159387,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", + "Filter1", "Add_a_column1", + "gops_intersect_1", + "Convert characters1", + "XY_Plot_1", "sam_pileup", - "gops_basecoverage_1", "Cut1", - "XY_Plot_1", - "Convert characters1", - "Filter1", - "gops_intersect_1", - "Paste1" + "gops_basecoverage_1" ], "update_time": "2012-12-06", "versions": 0 @@ -144145,11 +159417,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Add_a_column1", - "samtools_mpileup", - "Cut1", "gops_coverage_1", + "samtools_mpileup", "Filter1", + "Add_a_column1", + "Cut1", "column_join" ], "update_time": "2012-12-06", @@ -144171,24 +159443,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", "snp_mapping_using_wgs", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2012-12-03", "versions": -1 @@ -144211,10 +159483,10 @@ "illumina" ], "tools": [ + "fastq_stats", "qual_stats_boxplot", - "fastq_groomer", "fastq_quality_trimmer", - "fastq_stats" + "fastq_groomer" ], "update_time": "2012-12-03", "versions": 0 @@ -144235,9 +159507,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gops_subtract_1", "gops_intersect_1", - "snpEff" + "snpEff", + "gops_subtract_1" ], "update_time": "2012-11-28", "versions": 0 @@ -144258,10 +159530,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "check_snpeff_candidates", - "snpEff", "gatk_variant_combine", - "gatk_variant_select" + "gatk_variant_select", + "snpEff", + "check_snpeff_candidates" ], "update_time": "2012-11-28", "versions": 0 @@ -144282,22 +159554,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", - "gatk_realigner_target_creator", - "check_snpeff_candidates", + "fastq_stats", "gatk_indel_realigner", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2012-11-27", "versions": 1 @@ -144318,24 +159590,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", - "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", "snp_mapping_using_wgs", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", + "sam_bw_filter", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2012-11-26", "versions": 6 @@ -144345,9 +159617,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "400c1d170f073279", @@ -144362,9 +159634,9 @@ "for" ], "tools": [ - "fastqc", + "fasta_compute_length", "fastq_to_fasta_python", - "fasta_compute_length" + "fastqc" ], "update_time": "2012-11-13", "versions": 3 @@ -144374,9 +159646,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "fcce98489c8ca7a3", @@ -144389,13 +159661,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffdiff", - "fastq_trimmer", - "Show beginning1", "cufflinks", - "fastqc", + "Show beginning1", "tophat", - "cuffcompare" + "cuffcompare", + "fastqc", + "fastq_trimmer", + "cuffdiff" ], "update_time": "2012-11-09", "versions": 0 @@ -144416,23 +159688,23 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2012-10-15", "versions": 1 @@ -144453,24 +159725,24 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "picard_ARRG", + "qual_stats_boxplot", + "Filter1", + "snpEff", + "bedtools_genomecoveragebed_bedgraph", "sam_bw_filter", "ems_variant_density_mapping", - "gatk_realigner_target_creator", - "gatk_variant_select", - "check_snpeff_candidates", + "fastq_stats", "gatk_indel_realigner", + "gatk_variant_select", + "gatk_depth_of_coverage", "rgPicardMarkDups", - "fastq_stats", - "bedtools_genomecoveragebed_bedgraph", - "snpEff", - "qual_stats_boxplot", - "bwa_wrapper", "gatk_unified_genotyper", - "gatk_depth_of_coverage", - "Filter1", + "bwa_wrapper", "sam_to_bam", - "snpSift_filter" + "check_snpeff_candidates", + "snpSift_filter", + "picard_ARRG", + "gatk_realigner_target_creator" ], "update_time": "2012-10-15", "versions": 1 @@ -144493,8 +159765,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_to_fasta_python", "fasta_compute_length", + "fastq_to_fasta_python", "clustalw" ], "update_time": "2012-10-12", @@ -144516,16 +159788,16 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", - "fastq_groomer", - "cuffdiff", - "fastq_stats", + "bowtie_wrapper", "qual_stats_boxplot", - "sam_to_bam", "cufflinks", + "sam_bw_filter", + "fastq_stats", "tophat", - "bowtie_wrapper", - "cuffcompare" + "cuffcompare", + "sam_to_bam", + "cuffdiff", + "fastq_groomer" ], "update_time": "2012-10-11", "versions": 1 @@ -144571,12 +159843,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "fastq_groomer", - "samtools_flagstat", - "bwa_wrapper", "cufflinks", "tophat", - "bowtie_wrapper" + "bwa_wrapper", + "samtools_flagstat" ], "update_time": "2012-09-11", "versions": -1 @@ -144621,8 +159893,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "Convert characters1" + "Convert characters1", + "join1" ], "update_time": "2012-08-15", "versions": 4 @@ -144643,10 +159915,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffcompare", + "cufflinks", "tophat", - "fastq_groomer", - "cufflinks" + "cuffcompare", + "fastq_groomer" ], "update_time": "2012-07-31", "versions": 16 @@ -144668,11 +159940,11 @@ "tags": [], "tools": [ "Add_a_column1", - "join1", "Cut1", - "addValue", "Convert characters1", - "mergeCols1" + "join1", + "mergeCols1", + "addValue" ], "update_time": "2012-07-27", "versions": 4 @@ -144682,8 +159954,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", - "Statistical calculation" + "Statistical calculation", + "Variant calling" ], "edam_topic": [], "id": "e1211222348b4653", @@ -144717,10 +159989,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Cut1", + "comp1", "Filter1", - "subtract_query1", - "comp1" + "Cut1", + "subtract_query1" ], "update_time": "2012-06-28", "versions": 1 @@ -144790,8 +160062,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Filter1", - "Convert characters1" + "Convert characters1", + "Filter1" ], "update_time": "2012-06-24", "versions": 0 @@ -144812,9 +160084,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cshl_fastx_quality_statistics", "cshl_fastq_quality_boxplot", - "cshl_fastx_nucleotides_distribution", - "cshl_fastx_quality_statistics" + "cshl_fastx_nucleotides_distribution" ], "update_time": "2012-06-22", "versions": 0 @@ -144856,11 +160128,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2012-06-20", "versions": -1 @@ -144881,9 +160153,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cshl_fastx_quality_statistics", "cshl_fastq_quality_boxplot", - "cshl_fastx_nucleotides_distribution", - "cshl_fastx_quality_statistics" + "cshl_fastx_nucleotides_distribution" ], "update_time": "2012-06-19", "versions": 0 @@ -144904,11 +160176,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", "sort1", - "Grouping1", "Filter1", - "gops_join_1" + "gops_join_1", + "Grouping1", + "join1" ], "update_time": "2012-06-15", "versions": 5 @@ -144948,27 +160220,27 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_quality_trimmer", + "fastq_combiner", + "Cut1", + "fasta2tab", + "Grep1", + "join1", "fastq_trimmer", - "fastq_to_fasta_python", - "fasta_filter_by_length", - "sam2interval", - "Grouping1", - "mergeCols1", "bowtie_wrapper", "Add_a_column1", - "tab2fasta", - "join1", - "fastq_combiner", - "addValue", + "fastq_to_fasta_python", + "wc_gnu", + "gops_join_1", "Convert characters1", + "addValue", "cat1", + "fastq_quality_trimmer", "sam_bw_filter", - "fasta2tab", - "wc_gnu", - "Cut1", - "Grep1", - "gops_join_1" + "fasta_filter_by_length", + "tab2fasta", + "sam2interval", + "Grouping1", + "mergeCols1" ], "update_time": "2012-05-25", "versions": 0 @@ -144989,9 +160261,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "addValue", "Remove beginning1", - "comp1" + "comp1", + "addValue" ], "update_time": "2012-05-22", "versions": 8 @@ -145033,12 +160305,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "fastq_groomer", - "samtools_flagstat", - "bwa_wrapper", "cufflinks", "tophat", - "bowtie_wrapper" + "bwa_wrapper", + "samtools_flagstat" ], "update_time": "2012-05-03", "versions": -1 @@ -145059,12 +160331,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "fastq_groomer", - "samtools_flagstat", - "bwa_wrapper", "cufflinks", "tophat", - "bowtie_wrapper" + "bwa_wrapper", + "samtools_flagstat" ], "update_time": "2012-04-25", "versions": -1 @@ -145085,12 +160357,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "fastq_groomer", - "samtools_flagstat", - "bwa_wrapper", "cufflinks", "tophat", - "bowtie_wrapper" + "bwa_wrapper", + "samtools_flagstat" ], "update_time": "2012-04-16", "versions": 3 @@ -145111,17 +160383,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", - "sam_bw_filter", "cat1", + "Filter1", "Add_a_column1", - "sam_pileup", + "sam_bw_filter", + "pileup_parser", + "Grouping1", + "sam_to_bam", "join1", + "sam_pileup", "Cut1", - "addValue", - "Grouping1", - "Filter1", - "sam_to_bam" + "addValue" ], "update_time": "2012-04-03", "versions": 0 @@ -145143,11 +160415,11 @@ "tags": [], "tools": [ "gops_subtract_1", + "flanking_features_1", + "gops_join_1", "Count1", "join1", - "Cut1", - "flanking_features_1", - "gops_join_1" + "Cut1" ], "update_time": "2012-03-28", "versions": -1 @@ -145168,13 +160440,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", "cat1", - "Cut1", - "addValue", - "ChangeCase", + "Filter1", "mergeCols1", - "Filter1" + "Extract genomic DNA 1", + "ChangeCase", + "Cut1", + "addValue" ], "update_time": "2012-03-26", "versions": 2 @@ -145195,22 +160467,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", + "sort1", "Add_a_column1", - "pca1", "Show tail1", - "Count1", - "Cut1", - "join1", - "trimmer", - "sort1", - "addValue", + "Show beginning1", + "column_join", "Remove beginning1", "Convert characters1", - "Show beginning1", "Grouping1", - "column_join", - "Paste1" + "Count1", + "join1", + "pca1", + "Cut1", + "addValue", + "trimmer" ], "update_time": "2012-03-26", "versions": 1 @@ -145231,22 +160503,22 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "cat1", + "sort1", "Add_a_column1", - "pca1", "Show tail1", - "Count1", - "Cut1", - "join1", - "trimmer", - "sort1", - "addValue", + "Show beginning1", + "column_join", "Remove beginning1", "Convert characters1", - "Show beginning1", "Grouping1", - "column_join", - "Paste1" + "Count1", + "join1", + "pca1", + "Cut1", + "addValue", + "trimmer" ], "update_time": "2012-03-24", "versions": 13 @@ -145267,12 +160539,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "Count1", - "comp1", "sort1", - "addValue", - "Filter1" + "comp1", + "Count1", + "addValue" ], "update_time": "2012-03-16", "versions": 3 @@ -145293,10 +160565,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cuffcompare", + "cufflinks", "tophat", "cuffdiff", - "cufflinks" + "cuffcompare" ], "update_time": "2012-03-14", "versions": -1 @@ -145306,8 +160578,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -145322,17 +160594,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2012-03-13", @@ -145354,9 +160626,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "Cut1", "addValue", - "Paste1", "mergeCols1" ], "update_time": "2012-03-07", @@ -145378,8 +160650,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "addValue", - "wiggle2simple1" + "wiggle2simple1", + "addValue" ], "update_time": "2012-03-02", "versions": 2 @@ -145400,11 +160672,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", - "fastq_groomer", + "bowtie_wrapper", "fastq_filter", + "cshl_fastx_clipper", "sam_to_bam", - "bowtie_wrapper" + "fastq_groomer" ], "update_time": "2012-02-26", "versions": 2 @@ -145425,12 +160697,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", "cat1", + "Filter1", "Add_a_column1", + "pileup_parser", "sam_pileup", - "addValue", - "Filter1" + "addValue" ], "update_time": "2012-01-31", "versions": 3 @@ -145440,8 +160712,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -145456,17 +160728,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2012-01-25", @@ -145488,10 +160760,10 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bwa_wrapper", "peakcalling_macs", - "fastq_groomer", "sam_to_bam", - "bwa_wrapper" + "fastq_groomer" ], "update_time": "2012-01-19", "versions": 0 @@ -145513,9 +160785,9 @@ "tags": [], "tools": [ "CONVERTER_gff_to_bed_0", - "CONVERTER_interval_to_bed6_0", "CONVERTER_bed_to_genetrack_0", - "CONVERTER_interval_to_bedstrict_0" + "CONVERTER_interval_to_bedstrict_0", + "CONVERTER_interval_to_bed6_0" ], "update_time": "2011-12-01", "versions": -1 @@ -145525,8 +160797,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -145540,13 +160812,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", + "lca1", "Fetch Taxonomic Ranks", "Draw_phylogram", - "join1", - "lca1", - "t2t_report", - "Filter1", "megablast_wrapper", + "t2t_report", + "join1", "fasta_compute_length" ], "update_time": "2011-11-27", @@ -145569,9 +160841,9 @@ "tags": [], "tools": [ "pileup_parser", - "sam_pileup", + "bwa_wrapper", "sam_to_bam", - "bwa_wrapper" + "sam_pileup" ], "update_time": "2011-11-24", "versions": 0 @@ -145593,18 +160865,18 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "Add_a_column1", "sam_bw_filter", "pileup_parser", - "Add_a_column1", - "sam_pileup", "Grep1", + "bwa_wrapper", + "Grouping1", + "sam_to_bam", "join1", + "sam_pileup", "Cut1", - "addValue", - "Grouping1", - "bwa_wrapper", - "Filter1", - "sam_to_bam" + "addValue" ], "update_time": "2011-11-18", "versions": 25 @@ -145625,15 +160897,15 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", + "sort1", + "Show beginning1", "hyphy_nj_tree_wrapper1", "Interval2Maf1", + "gops_join_1", + "Extract genomic DNA 1", "Interval_Maf_Merged_Fasta2", "comp1", - "sort1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2011-11-16", "versions": 0 @@ -145655,9 +160927,9 @@ "tags": [], "tools": [ "CONVERTER_gff_to_bed_0", - "CONVERTER_interval_to_bed6_0", "CONVERTER_bed_to_genetrack_0", - "CONVERTER_interval_to_bedstrict_0" + "CONVERTER_interval_to_bedstrict_0", + "CONVERTER_interval_to_bed6_0" ], "update_time": "2011-11-16", "versions": -1 @@ -145678,11 +160950,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "LinearRegression1", - "join1", - "Grouping1", + "gops_join_1", "scatterplot_rpy", - "gops_join_1" + "Grouping1", + "join1", + "LinearRegression1" ], "update_time": "2011-11-16", "versions": 0 @@ -145727,13 +160999,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", "gops_subtract_1", - "featureCoverage1", "Cut1", - "addValue", + "featureCoverage1", "mergeCols1", - "Filter1" + "addValue" ], "update_time": "2011-11-14", "versions": 6 @@ -145754,8 +161026,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "join1", - "gops_intersect_1" + "gops_intersect_1", + "join1" ], "update_time": "2011-11-13", "versions": 2 @@ -145776,8 +161048,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "wc_gnu", - "gops_intersect_1" + "gops_intersect_1", + "wc_gnu" ], "update_time": "2011-11-04", "versions": 1 @@ -145820,14 +161092,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_groomer", - "cuffdiff", - "fastq_stats", "qual_stats_boxplot", - "bwa_wrapper", "cufflinks", + "fastq_stats", "tophat", - "cuffcompare" + "cuffcompare", + "bwa_wrapper", + "cuffdiff", + "fastq_groomer" ], "update_time": "2011-11-01", "versions": 8 @@ -145848,11 +161120,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2011-10-24", "versions": 2 @@ -145873,11 +161145,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", "pileup_parser", - "sam_pileup", - "Cut1", "sam_to_bam", - "bowtie_wrapper" + "sam_pileup", + "Cut1" ], "update_time": "2011-10-19", "versions": 3 @@ -145900,16 +161172,16 @@ "snp" ], "tools": [ - "join1", + "Filter1", "hgv_codingSnps", + "Grep1", + "gops_intersect_1", "gops_merge_1", - "hgv_sift", - "addValue", - "mergeCols1", - "Filter1", + "join1", "ctdBatch_1", - "Grep1", - "gops_intersect_1" + "mergeCols1", + "addValue", + "hgv_sift" ], "update_time": "2011-10-14", "versions": 6 @@ -145930,11 +161202,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2011-09-04", "versions": 2 @@ -145959,8 +161231,8 @@ "chip-seq" ], "tools": [ - "peakcalling_macs", "sort1", + "peakcalling_macs", "sam_to_bam", "bam_to_sam" ], @@ -145983,9 +161255,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "Cut1", "addValue", - "Paste1", "mergeCols1" ], "update_time": "2011-08-03", @@ -146029,9 +161301,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", "bowtie_wrapper", - "sam_to_bam" + "sam_to_bam", + "sam_bw_filter" ], "update_time": "2011-07-26", "versions": 13 @@ -146052,9 +161324,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "cshl_fastx_quality_statistics", "cshl_fastq_quality_boxplot", - "fastq_groomer", - "cshl_fastx_quality_statistics" + "fastq_groomer" ], "update_time": "2011-07-26", "versions": 0 @@ -146096,11 +161368,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "comp1", "sort1", - "Grouping1", "Show beginning1", - "gops_join_1" + "gops_join_1", + "comp1", + "Grouping1" ], "update_time": "2011-07-21", "versions": 0 @@ -146110,8 +161382,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -146126,17 +161398,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2011-06-30", @@ -146158,12 +161430,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "join1", - "Cut1", "comp1", "Grouping1", - "Filter1" + "join1", + "Cut1" ], "update_time": "2011-06-29", "versions": 7 @@ -146184,9 +161456,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Paste1", "Cut1", "addValue", - "Paste1", "mergeCols1" ], "update_time": "2011-06-28", @@ -146208,9 +161480,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "cshl_fastx_clipper", "fastq_filter", - "fastq_to_fasta_python" + "fastq_to_fasta_python", + "cshl_fastx_clipper" ], "update_time": "2011-06-21", "versions": 4 @@ -146220,8 +161492,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", "Database search", + "Phylogenetic tree visualisation", "ID mapping" ], "edam_topic": [], @@ -146236,17 +161508,17 @@ "tags": [], "tools": [ "cat1", + "Filter1", + "lca1", + "tab2fasta", "fasta2tab", "Fetch Taxonomic Ranks", "Draw_phylogram", - "tab2fasta", - "join1", - "lca1", + "megablast_wrapper", "t2t_report", - "Filter1", - "addValue", + "join1", "trim_reads", - "megablast_wrapper", + "addValue", "fasta_compute_length" ], "update_time": "2011-06-14", @@ -146280,10 +161552,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "a666aaaa32f62487", @@ -146300,13 +161572,13 @@ "bed" ], "tools": [ - "Extract genomic DNA 1", "Add_a_column1", + "Extract genomic DNA 1", + "EMBOSS: fuzznuc37", "gff2bed1", + "Convert characters1", "Cut1", - "EMBOSS: fuzznuc37", - "addValue", - "Convert characters1" + "addValue" ], "update_time": "2011-06-07", "versions": 7 @@ -146336,10 +161608,10 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Global alignment", "Sequence analysis", - "Local alignment", - "Sequence alignment" + "Sequence alignment", + "Global alignment", + "Local alignment" ], "edam_topic": [], "id": "6f836f4b71d399e7", @@ -146352,17 +161624,17 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "gops_basecoverage_1", - "Cut1", "tab2fasta", - "join1", - "comp1", + "EMBOSS: geecee41", "gops_cluster_1", "Remove beginning1", + "comp1", "Convert characters1", - "Filter1", - "EMBOSS: geecee41" + "join1", + "Cut1", + "gops_basecoverage_1" ], "update_time": "2011-05-05", "versions": 13 @@ -146385,9 +161657,9 @@ "biostar" ], "tools": [ - "join1", + "Filter1", "Add_a_column1", - "Filter1" + "join1" ], "update_time": "2011-04-21", "versions": 0 @@ -146408,19 +161680,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", - "sam_bw_filter", "cat1", + "Filter1", "Add_a_column1", - "sam_pileup", + "sam_bw_filter", + "pileup_parser", "Grep1", + "bwa_wrapper", + "Grouping1", + "sam_to_bam", "join1", + "sam_pileup", "Cut1", - "addValue", - "Grouping1", - "bwa_wrapper", - "Filter1", - "sam_to_bam" + "addValue" ], "update_time": "2011-03-24", "versions": 2 @@ -146441,14 +161713,14 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "sam_bw_filter", - "fastq_groomer", "cshl_fastx_quality_statistics", + "bowtie_wrapper", + "sam_bw_filter", "CONVERTER_Bam_Bai_0", + "cshl_fastq_quality_boxplot", "sam_to_bam", "CONVERTER_bam_to_summary_tree_0", - "bowtie_wrapper", - "cshl_fastq_quality_boxplot" + "fastq_groomer" ], "update_time": "2011-03-05", "versions": 0 @@ -146469,12 +161741,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Add_a_column1", - "gene2exon1", - "join1", "sort1", + "Add_a_column1", + "gops_join_1", "Grouping1", - "gops_join_1" + "join1", + "gene2exon1" ], "update_time": "2011-03-01", "versions": 1 @@ -146495,13 +161767,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "bowtie_wrapper", + "Filter1", "pileup_parser", - "fastq_groomer", + "sam_to_bam", "sam_pileup", "Cut1", - "sam_to_bam", - "Filter1", - "bowtie_wrapper" + "fastq_groomer" ], "update_time": "2011-02-24", "versions": 8 @@ -146522,9 +161794,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Grep1", "cat1", - "sort1", - "Grep1" + "sort1" ], "update_time": "2011-01-17", "versions": -1 @@ -146545,11 +161817,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bowtie_color_wrapper", + "peakcalling_macs", "sam_bw_filter", - "solid2fastq", + "bowtie_color_wrapper", "Count1", - "peakcalling_macs" + "solid2fastq" ], "update_time": "2011-01-17", "versions": -1 @@ -146570,8 +161842,8 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "gops_intersect_1", - "get_flanks1" + "get_flanks1", + "gops_intersect_1" ], "update_time": "2010-11-06", "versions": 1 @@ -146592,9 +161864,9 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Grep1", "cat1", - "sort1", - "Grep1" + "sort1" ], "update_time": "2010-11-03", "versions": 4 @@ -146619,11 +161891,11 @@ "faire" ], "tools": [ - "bowtie_color_wrapper", + "peakcalling_macs", "sam_bw_filter", - "solid2fastq", + "bowtie_color_wrapper", "Count1", - "peakcalling_macs" + "solid2fastq" ], "update_time": "2010-10-27", "versions": 20 @@ -146645,14 +161917,14 @@ "tags": [], "tools": [ "cat1", - "Cut1", - "join1", + "Filter1", "sort1", - "addValue", + "mergeCols1", "Remove beginning1", "Grouping1", - "mergeCols1", - "Filter1" + "join1", + "Cut1", + "addValue" ], "update_time": "2010-10-25", "versions": 2 @@ -146673,12 +161945,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "Add_a_column1", - "Cut1", + "Grep1", "join1", - "trimmer", - "Filter1", - "Grep1" + "Cut1", + "trimmer" ], "update_time": "2010-10-23", "versions": 10 @@ -146699,12 +161971,12 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "Extract genomic DNA 1", - "Add_a_column1", - "Cut1", "gops_coverage_1", "sort1", - "Filter1" + "Add_a_column1", + "Filter1", + "Extract genomic DNA 1", + "Cut1" ], "update_time": "2010-10-15", "versions": 0 @@ -146730,14 +162002,14 @@ "bowtie" ], "tools": [ + "bowtie_wrapper", + "Filter1", "pileup_parser", - "fastq_groomer", + "gops_intersect_1", + "sam_to_bam", "sam_pileup", "fastq_trimmer", - "sam_to_bam", - "Filter1", - "bowtie_wrapper", - "gops_intersect_1" + "fastq_groomer" ], "update_time": "2010-09-16", "versions": 8 @@ -146758,11 +162030,11 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "fastq_stats", + "bowtie_wrapper", "qual_stats_boxplot", - "sam_to_bam", + "fastq_stats", "solid_qual_boxplot", - "bowtie_wrapper" + "sam_to_bam" ], "update_time": "2010-09-01", "versions": 0 @@ -146806,9 +162078,9 @@ "tags": [], "tools": [ "cat1", - "join1", "Filter1", - "Grouping1" + "Grouping1", + "join1" ], "update_time": "2010-07-10", "versions": 3 @@ -146829,19 +162101,19 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", + "qual_stats_boxplot", "cat1", + "Filter1", "Add_a_column1", - "sam_pileup", - "Summary_Statistics1", - "Cut1", "fastq_stats", - "qual_stats_boxplot", - "sam_to_bam", - "bwa_wrapper", - "Filter1", + "pileup_parser", "Grep1", - "gops_join_1" + "gops_join_1", + "bwa_wrapper", + "Summary_Statistics1", + "sam_to_bam", + "sam_pileup", + "Cut1" ], "update_time": "2010-06-24", "versions": 0 @@ -146862,13 +162134,13 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ + "Filter1", "pileup_parser", - "sam_pileup", "Grep1", - "Summary_Statistics1", "bwa_wrapper", - "Filter1", - "sam_to_bam" + "Summary_Statistics1", + "sam_to_bam", + "sam_pileup" ], "update_time": "2010-06-24", "versions": 0 @@ -146889,18 +162161,18 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "pileup_parser", - "sam_bw_filter", "cat1", + "Filter1", "Add_a_column1", - "sam_pileup", + "sam_bw_filter", + "pileup_parser", "Grep1", - "Cut1", - "Summary_Statistics1", + "gops_join_1", "bwa_wrapper", - "Filter1", + "Summary_Statistics1", "sam_to_bam", - "gops_join_1" + "sam_pileup", + "Cut1" ], "update_time": "2010-06-11", "versions": 0 @@ -146922,10 +162194,10 @@ "tags": [], "tools": [ "fasta2tab", - "join1", - "Cut1", + "gops_join_1", "Convert characters1", - "gops_join_1" + "join1", + "Cut1" ], "update_time": "2010-06-08", "versions": 1 @@ -146947,10 +162219,10 @@ "tags": [], "tools": [ "cat1", + "Filter1", "Count1", - "Cut1", "join1", - "Filter1" + "Cut1" ], "update_time": "2010-05-09", "versions": 7 @@ -147014,16 +162286,76 @@ "source": "https://usegalaxy.org", "tags": [], "tools": [ - "bowtie_color_wrapper", "sam_bw_filter", - "solid2fastq", - "solid_qual_stats", + "bowtie_color_wrapper", + "solid_qual_boxplot", "sam2interval", - "solid_qual_boxplot" + "solid2fastq", + "solid_qual_stats" ], "update_time": "2010-02-01", "versions": 0 }, + { + "create_time": "2024-12-19", + "creators": [ + "Galaxy", + "VGP" + ], + "doi": "", + "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", + "Sequencing quality control", + "Phasing", + "Transcriptome assembly", + "k-mer counting", + "Read pre-processing", + "De-novo assembly", + "Sequence trimming", + "Sequence assembly validation", + "Validation", + "Data handling" + ], + "edam_topic": [], + "id": "9642aadb83c4f752", + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://usegalaxy.org.au/published/workflow?id=9642aadb83c4f752", + "name": "Assembly-Hifi-Trio-phasing-VGP5 (release v0.4)", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.org.au", + "tags": [ + "vgp", + "reviewed" + ], + "tools": [ + "__EXTRACT_DATASET__", + "tp_find_and_replace", + "join1", + "tp_grep_tool", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", + "Convert characters1", + "busco", + "cutadapt", + "hifiasm", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", + "Cut1", + "tp_awk_tool" + ], + "update_time": "2024-12-19", + "versions": 1 + }, { "create_time": "2024-09-23", "creators": [ @@ -147031,8 +162363,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence file editing" + "Sequence file editing", + "Data handling" ], "edam_topic": [], "id": "462beb964c99619d", @@ -147049,16 +162381,16 @@ ], "tools": [ "cat1", - "__CROSS_PRODUCT_FLAT__", + "param_value_from_file", "Add_a_column1", "wc_gnu", - "Cut1", - "param_value_from_file", + "__CROSS_PRODUCT_FLAT__", + "seqtk_seq", "cat_multiple", - "addValue", - "tp_text_file_with_recurring_lines", "map_param_value", - "seqtk_seq" + "tp_text_file_with_recurring_lines", + "Cut1", + "addValue" ], "update_time": "2024-12-13", "versions": 40 @@ -147070,16 +162402,16 @@ ], "doi": "", "edam_operation": [ - "Filtering", + "Visualisation", + "Statistical calculation", + "Formatting", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", - "Formatting", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "ba217a34d7e1b5ee", @@ -147095,22 +162427,22 @@ ], "tools": [ "msconvert", + "filter_tabular", + "Filter1", + "query_tabular", + "Cut1", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "tp_cat", + "Grep1", "search_gui", - "peptide_shaker", - "fasta_cli", - "Cut1", "ident_params", "Remove beginning1", - "query_tabular", "Grouping1", + "fasta_cli", + "fasta_merge_files_and_filter_unique_sequences", "dbbuilder", - "tp_cat", - "filter_tabular", - "Filter1", - "Grep1", - "maxquant" + "maxquant", + "peptide_shaker" ], "update_time": "2024-12-12", "versions": 1 @@ -147120,10 +162452,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment" + "Statistical calculation", + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "9cf3860659285656", @@ -147136,10 +162468,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "hisat2", "rna_star", - "trimmomatic" + "hisat2", + "trimmomatic", + "fastqc" ], "update_time": "2024-12-07", "versions": 18 @@ -147151,9 +162483,9 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "f547724fb0b2806a", @@ -147169,8 +162501,8 @@ "example" ], "tools": [ - "fastqc", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2024-12-05", "versions": 45 @@ -147183,20 +162515,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0af0ea50f1237952", @@ -147212,25 +162544,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -147243,20 +162575,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "e28ca83f14f4ede5", @@ -147272,25 +162604,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-12-05", "versions": 1 @@ -147315,17 +162647,17 @@ "name:clinicalmp" ], "tools": [ - "pepquery2", - "fasta_merge_files_and_filter_unique_sequences", + "uniprotxml_downloader", + "Filter1", "collapse_dataset", + "query_tabular", "Cut1", + "pepquery2", + "tp_cat", "Remove beginning1", - "query_tabular", "Grouping1", - "dbbuilder", - "Filter1", - "uniprotxml_downloader", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "dbbuilder" ], "update_time": "2024-11-28", "versions": 1 @@ -147353,8 +162685,8 @@ "name:clinicalmp" ], "tools": [ - "unipept", "Grep1", + "unipept", "msstatstmt" ], "update_time": "2024-11-28", @@ -147367,10 +162699,10 @@ ], "doi": "", "edam_operation": [ - "Protein identification", - "Expression analysis", "Target-Decoy", + "Protein identification", "de Novo sequencing", + "Expression analysis", "Tag-based peptide identification" ], "edam_topic": [], @@ -147422,14 +162754,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "749d8f2d26e0a111", @@ -147445,13 +162777,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-28", @@ -147464,10 +162796,10 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", "Statistical calculation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "a335b9c9103b57ad", @@ -147485,22 +162817,22 @@ "name:collection" ], "tools": [ - "Show tail1", - "kraken2", - "krakentools_beta_diversity", - "Cut1", + "Paste1", "collection_element_identifiers", - "regex1", "add_line_to_file", - "est_abundance", + "kraken2", + "regex1", + "krakentools_kreport2krona", "cat_multiple", - "Paste1", "taxonomy_krona_chart", "collection_column_join", - "krakentools_alpha_diversity", + "krakentools_combine_kreports", + "est_abundance", + "krakentools_beta_diversity", + "Cut1", "__RELABEL_FROM_FILE__", - "krakentools_kreport2krona", - "krakentools_combine_kreports" + "Show tail1", + "krakentools_alpha_diversity" ], "update_time": "2024-11-27", "versions": 130 @@ -147512,13 +162844,13 @@ ], "doi": "", "edam_operation": [ - "Sequence conversion", - "Aggregation", "Visualisation", - "DNA translation", "Sequence trimming", + "Taxonomic classification", + "DNA translation", "DNA transcription", - "Taxonomic classification" + "Sequence conversion", + "Aggregation" ], "edam_topic": [], "id": "ed3e48a73b5aaa56", @@ -147533,10 +162865,10 @@ "ga-public-workflow" ], "tools": [ - "seqkit_stats", "krakentools_kreport2krona", - "kraken2", - "taxonomy_krona_chart" + "seqkit_stats", + "taxonomy_krona_chart", + "kraken2" ], "update_time": "2024-11-25", "versions": 24 @@ -147548,10 +162880,10 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -147568,8 +162900,8 @@ "example" ], "tools": [ - "quast", - "busco" + "busco", + "quast" ], "update_time": "2024-11-22", "versions": 5 @@ -147581,14 +162913,14 @@ ], "doi": "", "edam_operation": [ - "Protein feature detection", - "Formatting", - "Structure visualisation", - "Genome visualisation", "Genome annotation", - "Sequence motif recognition", "Gene prediction", + "Sequence motif recognition", + "Protein feature detection", + "Structure visualisation", + "Formatting", "Pathway visualisation", + "Genome visualisation", "Repeat sequence detection" ], "edam_topic": [], @@ -147606,21 +162938,21 @@ "ga-public-workflow" ], "tools": [ - "interproscan", - "funannotate_annotate", "jcvi_gff_stats", "picard_NormalizeFasta", - "fgenesh_split", + "fgenesh_annotate", + "funannotate_clean", "helixer", "repeatmodeler", - "tp_sed_tool", - "tp_grep_tool", - "fgenesh_annotate", + "fgenesh_split", "repeatmasker_wrapper", - "funannotate_clean", - "fgenesh_merge", + "tp_grep_tool", + "jbrowse2", + "tp_sed_tool", + "interproscan", "funannotate_predict", - "jbrowse2" + "funannotate_annotate", + "fgenesh_merge" ], "update_time": "2024-11-21", "versions": 54 @@ -147632,9 +162964,9 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", "Sequence assembly validation", "Scaffolding", - "Genome assembly", "Transcriptome assembly" ], "edam_topic": [], @@ -147652,12 +162984,12 @@ "ga-public-workflow" ], "tools": [ - "ragtag", - "ncbi_tblastn_wrapper", "ncbi_makeblastdb", + "ncbi_tblastn_wrapper", + "ragtag", + "plot_ragtag_paf", "busco", - "chromeister", - "plot_ragtag_paf" + "chromeister" ], "update_time": "2024-11-21", "versions": 28 @@ -147669,16 +163001,16 @@ ], "doi": "", "edam_operation": [ - "Mapping assembly", - "De-novo assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", "Sequence contamination filtering", "Statistical calculation", "Genome assembly", - "Mapping", - "Sequence trimming" + "Sequence assembly visualisation", + "Mapping assembly", + "Sequencing quality control", + "De-novo assembly", + "Sequence composition calculation", + "Sequence trimming", + "Mapping" ], "edam_topic": [], "id": "f2541030f6d70b59", @@ -147695,12 +163027,12 @@ "ga-public-workflow" ], "tools": [ - "bandage_image", + "get_organelle_from_reads", "fasta-stats", "fastp", - "get_organelle_from_reads", - "shovill", - "fastqc" + "bandage_image", + "fastqc", + "shovill" ], "update_time": "2024-11-21", "versions": 29 @@ -147737,9 +163069,9 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "bc4e3115586cbe62", @@ -147755,14 +163087,14 @@ "example" ], "tools": [ - "fastqc", + "param_value_from_file", "Add_a_column1", "wc_gnu", - "param_value_from_file", - "pick_value", "compose_text_param", + "map_param_value", "tp_text_file_with_recurring_lines", - "map_param_value" + "fastqc", + "pick_value" ], "update_time": "2024-11-21", "versions": 15 @@ -147788,11 +163120,11 @@ "example" ], "tools": [ - "Add_a_column1", "param_value_from_file", - "pick_value", + "Add_a_column1", + "map_param_value", "tp_text_file_with_recurring_lines", - "map_param_value" + "pick_value" ], "update_time": "2024-11-21", "versions": 16 @@ -147804,11 +163136,11 @@ "edam_operation": [ "De-novo assembly", "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", "Statistical calculation", "Genome assembly", + "Sequence assembly visualisation", "Mapping assembly", + "Sequencing quality control", "Cross-assembly" ], "edam_topic": [], @@ -147824,15 +163156,15 @@ "genome_assembly" ], "tools": [ - "porechop", - "collapse_dataset", "flye", - "bandage_image", + "bandage_info", "nanofilt", + "collapse_dataset", "fasta-stats", - "fastqc", + "porechop", "split_file_to_collection", - "bandage_info" + "bandage_image", + "fastqc" ], "update_time": "2024-11-21", "versions": 50 @@ -147862,12 +163194,12 @@ "ga-public-workflow" ], "tools": [ - "hifiadapterfilt", + "bandage_info", + "fasta-stats", "gfa_to_fa", "bandage_image", - "fasta-stats", - "hifiasm", - "bandage_info" + "hifiadapterfilt", + "hifiasm" ], "update_time": "2024-11-21", "versions": 10 @@ -147881,11 +163213,11 @@ "edam_operation": [ "De-novo assembly", "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", "Statistical calculation", "Genome assembly", + "Sequence assembly visualisation", "Mapping assembly", + "Sequencing quality control", "Cross-assembly" ], "edam_topic": [], @@ -147903,15 +163235,15 @@ "ga-public-workflow" ], "tools": [ - "porechop", - "collapse_dataset", "flye", - "bandage_image", + "bandage_info", "nanofilt", + "collapse_dataset", "fasta-stats", - "fastqc", + "porechop", "split_file_to_collection", - "bandage_info" + "bandage_image", + "fastqc" ], "update_time": "2024-11-21", "versions": 5 @@ -147941,12 +163273,12 @@ "ga-public-workflow" ], "tools": [ - "hifiadapterfilt", + "bandage_info", + "fasta-stats", "gfa_to_fa", "bandage_image", - "fasta-stats", - "hifiasm", - "bandage_info" + "hifiadapterfilt", + "hifiasm" ], "update_time": "2024-11-21", "versions": 1 @@ -147958,10 +163290,10 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "8215e0eb265e03a3", @@ -147978,8 +163310,8 @@ "tsi" ], "tools": [ - "picard_SamToFastq", "fastqc", + "picard_SamToFastq", "samtools_flagstat" ], "update_time": "2024-11-21", @@ -147992,13 +163324,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -148016,18 +163348,18 @@ "tsi" ], "tools": [ - "bellerophon", + "bwa_mem2", "__EXTRACT_DATASET__", - "ggplot2_point", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", + "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-11-21", "versions": 1 @@ -148040,14 +163372,14 @@ ], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "5cd804644a34c8fd", @@ -148064,23 +163396,23 @@ "tsi" ], "tools": [ + "Paste1", "cat1", + "filter_tabular", "Add_a_column1", + "fastq_to_fasta_python", "datamash_transpose", - "tp_replace_in_column", - "meryl", + "fasta-stats", + "merqury", "Cut1", - "add_line_to_file", - "quast", - "tp_grep_tool", + "meryl", "tp_sed_tool", - "fasta-stats", "Convert characters1", + "quast", "busco", - "filter_tabular", - "fastq_to_fasta_python", - "Paste1", - "merqury" + "tp_replace_in_column", + "tp_grep_tool", + "add_line_to_file" ], "update_time": "2024-11-21", "versions": 3 @@ -148094,11 +163426,11 @@ "edam_operation": [ "De-novo assembly", "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly visualisation", "Statistical calculation", "Genome assembly", + "Sequence assembly visualisation", "Mapping assembly", + "Sequencing quality control", "Cross-assembly" ], "edam_topic": [], @@ -148116,15 +163448,15 @@ "tsi" ], "tools": [ - "porechop", - "collapse_dataset", "flye", - "bandage_image", + "bandage_info", "nanofilt", + "collapse_dataset", "fasta-stats", - "fastqc", + "porechop", "split_file_to_collection", - "bandage_info" + "bandage_image", + "fastqc" ], "update_time": "2024-11-21", "versions": 1 @@ -148137,8 +163469,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence file editing" + "Sequence file editing", + "Data handling" ], "edam_topic": [], "id": "5cfea39918e8632d", @@ -148155,18 +163487,18 @@ "tsi" ], "tools": [ + "Paste1", + "tab2fasta", + "seqtk_seq", + "Cut1", + "tp_replace_in_line", + "seqtk_subseq", "fasta2tab", "tp_sort_header_tool", - "seqtk_subseq", - "tp_awk_tool", - "Cut1", - "tab2fasta", - "tp_grep_tool", "tp_sed_tool", - "tp_replace_in_line", - "seqtk_seq", - "fasta_compute_length", - "Paste1" + "tp_grep_tool", + "tp_awk_tool", + "fasta_compute_length" ], "update_time": "2024-11-21", "versions": 2 @@ -148179,12 +163511,12 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Scaffolding", + "Coding region prediction", "De-novo assembly", "Genome assembly", - "Coding region prediction", "de Novo sequencing", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -148202,9 +163534,9 @@ "tsi" ], "tools": [ - "transdecoder", + "tp_sed_tool", "busco", - "tp_sed_tool" + "transdecoder" ], "update_time": "2024-11-21", "versions": 2 @@ -148217,8 +163549,8 @@ ], "doi": "", "edam_operation": [ - "Mapping", "RNA-Seq analysis", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -148236,14 +163568,14 @@ "tsi" ], "tools": [ - "seq_filter_by_id", - "cpat", - "tp_cut_tool", + "Filter1", "stringtie_merge", + "gtftobed12", "tp_sed_tool", + "tp_cut_tool", + "cpat", "bedtools_getfastabed", - "gtftobed12", - "Filter1" + "seq_filter_by_id" ], "update_time": "2024-11-21", "versions": 2 @@ -148289,10 +163621,10 @@ ], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "8b5897305dcaf076", @@ -148311,12 +163643,12 @@ "tools": [ "__EXTRACT_DATASET__", "trimmomatic", - "Cut1", - "Remove beginning1", "multiqc", - "fastqc", + "tp_cat", + "Remove beginning1", "tp_replace_in_column", - "tp_cat" + "fastqc", + "Cut1" ], "update_time": "2024-11-21", "versions": 2 @@ -148347,9 +163679,9 @@ "tsi" ], "tools": [ - "repeatmasker_wrapper", + "tp_sed_tool", "repeatmodeler", - "tp_sed_tool" + "repeatmasker_wrapper" ], "update_time": "2024-11-21", "versions": 2 @@ -148363,9 +163695,9 @@ "doi": "", "edam_operation": [ "Sequence assembly validation", - "Transcriptome assembly", "Scaffolding", - "Genome assembly" + "Genome assembly", + "Transcriptome assembly" ], "edam_topic": [], "id": "49b253f75ab6f38f", @@ -148382,11 +163714,11 @@ "tsi" ], "tools": [ - "fgenesh_get_proteins", + "fgenesh_annotate", "jcvi_gff_stats", + "fgenesh_get_proteins", "fgenesh_get_mrnas_gc", "fgenesh_split", - "fgenesh_annotate", "busco", "fgenesh_merge" ], @@ -148400,8 +163732,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "28705b86e0595ded", @@ -148417,20 +163749,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-21", "versions": 1 @@ -148442,8 +163774,8 @@ ], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "a9e59d38c6c710bc", @@ -148459,20 +163791,20 @@ "rnaseq" ], "tools": [ - "ggplot2_heatmap2", - "volcanoplot", - "tp_awk_tool", - "join1", - "Cut1", "param_value_from_file", - "tp_sed_tool", - "pick_value", "Filter1", "compose_text_param", - "tp_text_file_with_recurring_lines", + "tp_awk_tool", + "tp_cat", + "tp_sed_tool", "deg_annotate", - "deseq2", - "tp_cat" + "volcanoplot", + "tp_text_file_with_recurring_lines", + "join1", + "Cut1", + "ggplot2_heatmap2", + "pick_value", + "deseq2" ], "update_time": "2024-11-21", "versions": 1 @@ -148510,10 +163842,10 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "8e28c3b252062b3b", @@ -148527,12 +163859,12 @@ "tags": [], "tools": [ "ip_binary_to_labelimage", - "ip_overlay_images", - "ip_count_objects", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", - "ip_threshold", - "ip_histogram_equalization" + "ip_count_objects", + "ip_overlay_images", + "ip_threshold" ], "update_time": "2024-11-21", "versions": 1 @@ -148545,14 +163877,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "7c22d726e1716f4b", @@ -148568,15 +163900,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-21", "versions": 1 @@ -148589,14 +163921,14 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence contamination filtering", + "Validation", "Sequence alignment", + "Transcriptome assembly", "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ccfae75390038ced", @@ -148612,15 +163944,15 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "stringtie", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", - "__FLATTEN__" + "__FLATTEN__", + "rna_star", + "stringtie" ], "update_time": "2024-11-21", "versions": 1 @@ -148633,14 +163965,14 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", + "Validation", + "Sequence alignment", "Transcriptome assembly", - "RNA-Seq analysis", + "RNA-Seq quantification", + "Read summarisation", "Sequencing quality control", - "Sequence alignment", - "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c8d18e2c03dca796", @@ -148656,13 +163988,13 @@ "transcriptomics" ], "tools": [ - "rna_star", + "cufflinks", "featurecounts", - "fastp", "compose_text_param", + "fastp", "multiqc", - "cufflinks", "map_param_value", + "rna_star", "stringtie" ], "update_time": "2024-11-21", @@ -148691,13 +164023,13 @@ ], "tools": [ "arriba_get_filters", - "rna_star", - "tp_awk_tool", - "tab2fasta", "regex1", + "tab2fasta", "arriba", + "CONVERTER_gz_to_uncompressed", + "rna_star", "query_tabular", - "CONVERTER_gz_to_uncompressed" + "tp_awk_tool" ], "update_time": "2024-11-08", "versions": 1 @@ -148725,13 +164057,13 @@ ], "tools": [ "arriba_get_filters", - "rna_star", - "tp_awk_tool", - "tab2fasta", "regex1", + "tab2fasta", "arriba", + "CONVERTER_gz_to_uncompressed", + "rna_star", "query_tabular", - "CONVERTER_gz_to_uncompressed" + "tp_awk_tool" ], "update_time": "2024-11-06", "versions": 2 @@ -148743,14 +164075,14 @@ ], "doi": "", "edam_operation": [ + "Genome annotation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Genome assembly", "Sequence assembly visualisation", - "Genome annotation", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Validation", + "Sequencing quality control", + "Taxonomic classification" ], "edam_topic": [], "id": "52065a4100b11184", @@ -148763,14 +164095,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", "kraken2", "trimmomatic", - "bandage_image", - "fasta-stats", - "shovill", "funannotate_clean", - "multiqc" + "fasta-stats", + "multiqc", + "bandage_image", + "fastqc", + "shovill" ], "update_time": "2024-11-04", "versions": 6 @@ -148796,13 +164128,13 @@ "name:neoantigen" ], "tools": [ + "Filter1", "pepquery2", "table_compute", - "Cut1", "Remove beginning1", - "query_tabular", "iedb_api", - "Filter1" + "query_tabular", + "Cut1" ], "update_time": "2024-11-04", "versions": 1 @@ -148831,10 +164163,10 @@ "name:neoantigen" ], "tools": [ - "tp_awk_tool", "query_tabular", - "optitype", - "seq2hla" + "seq2hla", + "tp_awk_tool", + "optitype" ], "update_time": "2024-11-04", "versions": 1 @@ -148859,11 +164191,11 @@ "name:neoantigen" ], "tools": [ - "pep_pointer", "regexColumn1", "tab2fasta", - "query_tabular", - "Convert characters1" + "Convert characters1", + "pep_pointer", + "query_tabular" ], "update_time": "2024-11-04", "versions": 1 @@ -148892,9 +164224,9 @@ ], "tools": [ "msconvert", - "pepquery2", "tab2fasta", "ncbi_blastp_wrapper", + "pepquery2", "query_tabular" ], "update_time": "2024-11-04", @@ -148920,12 +164252,12 @@ "name:neoantigen" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", + "fragpipe", "collapse_dataset", - "validate_fasta_database", "query_tabular", - "fragpipe", - "Grep1" + "validate_fasta_database", + "Grep1", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2024-11-04", "versions": 1 @@ -148937,12 +164269,12 @@ ], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "0ebaaecf61dfc921", @@ -148957,21 +164289,21 @@ "name:neoantigen" ], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", - "filter_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "CONVERTER_gz_to_uncompressed", - "custom_pro_db", - "tp_cat" + "fasta_merge_files_and_filter_unique_sequences", + "gffcompare", + "stringtie", + "hisat2", + "bed_to_protein_map", + "custom_pro_db" ], "update_time": "2024-11-04", "versions": 1 @@ -148992,11 +164324,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "sklearn_build_pipeline", - "sklearn_ensemble", - "sklearn_generalized_linear", "sklearn_searchcv", - "plotly_regression_performance_plots" + "plotly_regression_performance_plots", + "sklearn_generalized_linear", + "sklearn_build_pipeline", + "sklearn_ensemble" ], "update_time": "2024-11-02", "versions": 0 @@ -149008,14 +164340,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "c38b998d3e90c329", @@ -149032,19 +164364,19 @@ "haploid" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "collapse_dataset", - "tp_awk_tool", - "snpSift_extractFields", - "samtools_view", - "snpEff_build_gb", - "snpEff", "samtools_stats", - "fastp", + "snpEff", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "fastp", + "multiqc", + "bwa_mem", + "snpEff_build_gb", "lofreq_call", - "multiqc" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2024-10-31", "versions": 1 @@ -149077,24 +164409,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-10-31", "versions": 1 @@ -149155,13 +164487,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -149175,11 +164507,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2024-10-28", @@ -149190,13 +164522,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -149210,11 +164542,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "multiqc", + "velvetg", "velveth", - "quast", "fastq_paired_end_interlacer", - "velvetg", - "multiqc", + "quast", "fastqc" ], "update_time": "2024-10-27", @@ -149225,13 +164557,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -149245,11 +164577,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2024-10-27", @@ -149260,9 +164592,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0ed947e76a69028b", @@ -149275,8 +164607,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2024-10-22", "versions": 0 @@ -149286,16 +164618,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "baa763dbdf6afb71", @@ -149311,26 +164643,26 @@ "artic" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "__UNZIP_COLLECTION__", - "fastp", + "trimmomatic", + "fastqc", "lofreq_call", + "qualimap_bamqc", + "multiqc", "lofreq_indelqual", - "fastqc", - "ivar_removereads", - "vcfvcfintersect", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "__UNZIP_COLLECTION__", + "lofreq_viterbi", "tp_replace_in_line", - "samtools_stats", + "vcfvcfintersect", "__ZIP_COLLECTION__", - "qualimap_bamqc", - "__FLATTEN__", - "ivar_trim", + "snpeff_sars_cov_2", + "samtools_stats", "lofreq_filter", - "bwa_mem", - "trimmomatic", - "lofreq_viterbi", - "multiqc" + "fastp", + "ivar_removereads" ], "update_time": "2024-10-22", "versions": 1 @@ -149342,11 +164674,11 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", + "Pairwise sequence alignment", "Sequence alignment analysis", - "Scaffolding", "Genome assembly", - "Pairwise sequence alignment", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -149365,10 +164697,10 @@ "blobtools" ], "tools": [ - "bg_diamond", "minimap2", + "blobtoolkit", "busco", - "blobtoolkit" + "bg_diamond" ], "update_time": "2024-10-17", "versions": 20 @@ -149378,10 +164710,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -149401,8 +164733,8 @@ "pairedreads" ], "tools": [ - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-10-04", "versions": 1 @@ -149414,14 +164746,14 @@ ], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "b0a79310e0dc3fb4", @@ -149436,8 +164768,8 @@ "name:clinicalmp" ], "tools": [ - "Cut1", "Grep1", + "Cut1", "Grouping1", "maxquant" ], @@ -149465,20 +164797,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-10-03", "versions": 1 @@ -149490,14 +164822,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "fe5542c99cdc57ce", @@ -149514,26 +164846,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-10-03", "versions": 1 @@ -149543,16 +164875,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "d35d05be576e8b13", @@ -149568,26 +164900,26 @@ "artic" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "__UNZIP_COLLECTION__", - "fastp", + "trimmomatic", + "fastqc", "lofreq_call", + "qualimap_bamqc", + "multiqc", "lofreq_indelqual", - "fastqc", - "ivar_removereads", - "vcfvcfintersect", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "__UNZIP_COLLECTION__", + "lofreq_viterbi", "tp_replace_in_line", - "samtools_stats", + "vcfvcfintersect", "__ZIP_COLLECTION__", - "qualimap_bamqc", - "__FLATTEN__", - "ivar_trim", + "snpeff_sars_cov_2", + "samtools_stats", "lofreq_filter", - "bwa_mem", - "trimmomatic", - "lofreq_viterbi", - "multiqc" + "fastp", + "ivar_removereads" ], "update_time": "2024-10-02", "versions": 2 @@ -149603,11 +164935,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "738350fc2ca69c0b", @@ -149655,9 +164987,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-26", "versions": 1 @@ -149669,14 +165001,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ccc6602623583bcc", @@ -149691,14 +165023,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -149710,14 +165042,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "56bda8e4b0018e03", @@ -149732,14 +165064,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -149751,15 +165083,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "ce7106593536f900", @@ -149774,13 +165106,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -149792,15 +165124,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "fa87a22c8dcd8d78", @@ -149815,13 +165147,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-26", "versions": 1 @@ -149833,17 +165165,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2980172ed0226b59", @@ -149858,15 +165190,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-26", "versions": 1 @@ -149876,9 +165208,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d018214e901419c9", @@ -149901,12 +165233,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Sequence contamination filtering", + "Sequence composition calculation", "Statistical calculation", "Genome assembly", - "Sequence composition calculation", - "Sequencing quality control" + "Sequencing quality control", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "d78f885b4b86635f", @@ -149922,11 +165254,11 @@ "bacterial" ], "tools": [ - "abricate", "fasta-stats", + "abricate", "fastp", - "shovill", - "fastqc" + "fastqc", + "shovill" ], "update_time": "2024-09-24", "versions": 1 @@ -149936,9 +165268,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -149965,10 +165297,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -149983,10 +165315,10 @@ "tags": [], "tools": [ "qiime2__diversity__beta_group_significance", - "qiime2_core__tools__import", "qiime2__diversity__alpha_group_significance", - "qiime2__diversity__core_metrics_phylogenetic", - "__BUILD_LIST__" + "__BUILD_LIST__", + "qiime2_core__tools__import", + "qiime2__diversity__core_metrics_phylogenetic" ], "update_time": "2024-09-19", "versions": 1 @@ -150022,9 +165354,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "131636a795bac485", @@ -150042,8 +165374,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-09-19", @@ -150060,12 +165392,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "b60922a253df6654", @@ -150083,28 +165415,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-09-19", "versions": 1 @@ -150118,19 +165450,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "69d91340fc7effa2", @@ -150149,23 +165481,23 @@ "name:iwc" ], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -150179,15 +165511,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "084bb76cf47d7060", @@ -150205,18 +165537,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-09-19", "versions": 1 @@ -150229,8 +165561,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "9016b2be61f89053", @@ -150243,18 +165575,18 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150267,8 +165599,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "2fee25e188531691", @@ -150281,18 +165613,18 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "param_value_from_file", + "sort1", "Add_a_column1", - "ggplot2_point", + "addName", "collapse_dataset", - "tp_awk_tool", + "compose_text_param", "Cut1", - "param_value_from_file", + "gfastats", + "ggplot2_point", "datamash_ops", - "sort1", "addValue", - "compose_text_param", - "addName", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150305,10 +165637,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150323,8 +165655,8 @@ "tags": [], "tools": [ "qiime2__metadata__tabulate", - "qiime2__dada2__denoise_paired", "qiime2__feature_table__tabulate_seqs", + "qiime2__dada2__denoise_paired", "qiime2__feature_table__summarize" ], "update_time": "2024-09-19", @@ -150338,10 +165670,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150371,10 +165703,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150390,8 +165722,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -150405,10 +165737,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150424,8 +165756,8 @@ "tools": [ "collection_element_identifiers", "regex1", - "qiime2_core__tools__import", "qiime2__demux__summarize", + "qiime2_core__tools__import", "__RELABEL_FROM_FILE__" ], "update_time": "2024-09-19", @@ -150439,10 +165771,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150457,8 +165789,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_paired", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -150471,10 +165803,10 @@ ], "doi": "", "edam_operation": [ + "Visualisation", "Sequencing quality control", "Phylogenetic analysis", "Demultiplexing", - "Visualisation", "Taxonomic classification" ], "edam_topic": [], @@ -150489,8 +165821,8 @@ "tags": [], "tools": [ "qiime2__demux__emp_single", - "qiime2_core__tools__import", - "qiime2__demux__summarize" + "qiime2__demux__summarize", + "qiime2_core__tools__import" ], "update_time": "2024-09-19", "versions": 1 @@ -150503,8 +165835,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "1016f17b77a8216d", @@ -150519,17 +165851,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-09-19", "versions": 1 @@ -150542,16 +165874,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "7168c01be9997823", @@ -150566,17 +165898,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150589,16 +165921,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "543fb2d9431a7e13", @@ -150613,17 +165945,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150636,16 +165968,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "a209f43d8a3cc853", @@ -150660,20 +165992,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150686,16 +166018,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0df25e2dbd5e8ed5", @@ -150710,20 +166042,20 @@ "vgp_curated" ], "tools": [ + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", - "tp_awk_tool", - "Cut1", + "tp_find_and_replace", + "merqury", + "tp_grep_tool", + "gfastats", + "busco", "join1", "tp_cut_tool", - "param_value_from_file", - "tp_grep_tool", - "tp_find_and_replace", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -150854,9 +166186,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-19", "versions": 1 @@ -150887,9 +166219,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-19", "versions": 1 @@ -150920,9 +166252,9 @@ "name:single-cell" ], "tools": [ + "pick_value", "tp_awk_tool", - "cite_seq_count", - "pick_value" + "cite_seq_count" ], "update_time": "2024-09-19", "versions": 1 @@ -150951,14 +166283,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -150986,17 +166318,17 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", - "gfastats", - "Cut1", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_sed_tool", "tp_grep_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "tp_cat", + "gfastats", + "tp_sed_tool", + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -151024,15 +166356,15 @@ "vgp_curated" ], "tools": [ + "Filter1", "kraken2", - "parse_mito_blast", + "ncbi_blastn_wrapper", + "tp_cat", "gfastats", - "Cut1", "tp_sed_tool", - "ncbi_blastn_wrapper", - "Filter1", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "Cut1", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-09-19", "versions": 1 @@ -151046,20 +166378,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "8dd86497bc15d981", @@ -151075,23 +166407,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151105,20 +166437,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "319e9d693fac8dce", @@ -151134,23 +166466,23 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151164,20 +166496,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "5f4f874e49515555", @@ -151193,26 +166525,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151226,20 +166558,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "c6a71573a299eb3a", @@ -151255,26 +166587,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151288,20 +166620,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "60c0dec52cdca708", @@ -151317,26 +166649,26 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_sed_tool", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_sed_tool", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151349,20 +166681,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "ad10cd704268dcf0", @@ -151378,22 +166710,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151406,20 +166738,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1eb3e1452c672480", @@ -151435,22 +166767,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151463,20 +166795,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fe1e7fa0bc437ed8", @@ -151492,22 +166824,22 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", + "bandage_image", "Convert characters1", "busco", - "multiqc", - "cutadapt", + "tp_easyjoin_tool", + "tp_grep_tool", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151520,20 +166852,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "371c9892d261cee2", @@ -151549,25 +166881,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151580,8 +166912,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "87bbf9408b3f2a32", @@ -151596,11 +166928,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -151613,8 +166945,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "02f2a556e77eed14", @@ -151629,12 +166961,12 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", - "tp_find_and_replace", "param_value_from_file", - "gfastats" + "tp_find_and_replace", + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-09-19", "versions": 1 @@ -151661,8 +166993,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -151689,8 +167021,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -151717,8 +167049,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2024-09-19", "versions": 1 @@ -151731,16 +167063,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "06564b19b0655c19", @@ -151756,16 +167088,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151778,16 +167110,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "c556c2270200801d", @@ -151803,16 +167135,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151825,16 +167157,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0810be3d7d2b0322", @@ -151850,20 +167182,20 @@ ], "tools": [ "cat1", + "param_value_from_file", "Add_a_column1", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "merqury", "gfastats", - "Cut1", - "tp_awk_tool", + "busco", "join1", - "param_value_from_file", "tp_cut_tool", - "tp_find_and_replace", "minimap2", - "merqury", - "compose_text_param", - "busco", - "purge_dups" + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -151876,13 +167208,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -151898,19 +167230,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -151923,13 +167255,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -151945,19 +167277,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -151970,13 +167302,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -151992,20 +167324,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -152018,13 +167350,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -152040,20 +167372,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -152066,13 +167398,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -152088,20 +167420,20 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -152114,13 +167446,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -152136,21 +167468,21 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "tp_find_and_replace", + "compose_text_param", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_find_and_replace", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "compose_text_param", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-09-19", "versions": 1 @@ -152163,8 +167495,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "5e3ff382ab802baf", @@ -152177,8 +167509,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -152191,8 +167523,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "d6521e6c247eeaaf", @@ -152205,8 +167537,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -152219,8 +167551,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "51aaafbd00b91717", @@ -152233,8 +167565,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -152247,8 +167579,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "579da54989f5d55c", @@ -152261,8 +167593,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -152275,8 +167607,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "2436bc493e76f438", @@ -152289,8 +167621,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "baredsc_combine_2d", - "baredsc_2d" + "baredsc_2d", + "baredsc_combine_2d" ], "update_time": "2024-09-19", "versions": 1 @@ -152303,8 +167635,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "ac4799c5009f98d3", @@ -152331,8 +167663,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "481c666fbc7ffa02", @@ -152359,8 +167691,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "b73280eaeb77a0a9", @@ -152387,8 +167719,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "31a664d151978dc6", @@ -152415,8 +167747,8 @@ "doi": "", "edam_operation": [ "Differential gene expression profiling", - "Data retrieval", - "Expression correlation analysis" + "Expression correlation analysis", + "Data retrieval" ], "edam_topic": [], "id": "d01ff75a4943fa79", @@ -152443,19 +167775,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "9804030358c3f844", @@ -152471,21 +167803,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152498,19 +167830,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fa37223950a91f34", @@ -152526,21 +167858,21 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "pick_value", + "gfastats", "merqury", "Convert characters1", "busco", - "multiqc", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "pick_value", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152553,20 +167885,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "63789b6f82172679", @@ -152582,25 +167914,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152613,20 +167945,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", + "Scaffolding", "Sequencing quality control", "Phasing", - "Sequence assembly visualisation", + "Transcriptome assembly", "k-mer counting", - "Sequence assembly validation", - "Scaffolding", - "Primer removal", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "b5131e3a0ef2676e", @@ -152642,25 +167974,25 @@ "reviewed" ], "tools": [ - "bandage_image", - "tp_grep_tool", - "gfastats", "__EXTRACT_DATASET__", - "tp_cut_tool", "tp_find_and_replace", - "tp_replace_in_line", - "pick_value", - "Add_a_column1", "join1", + "tp_grep_tool", "param_value_from_file", + "Add_a_column1", + "multiqc", + "gfastats", "Convert characters1", "busco", + "cutadapt", "hifiasm", - "tp_awk_tool", + "pick_value", + "merqury", + "tp_replace_in_line", + "bandage_image", + "tp_cut_tool", "Cut1", - "multiqc", - "cutadapt", - "merqury" + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152673,17 +168005,17 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Read mapping", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Local alignment", - "Sequence alignment", + "Generation", "Genome indexing", - "Sequence contamination filtering", - "Global alignment", + "Sequence alignment analysis", "Sequence analysis", - "Generation", - "Validation" + "Global alignment", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "6b1b0a945d367b4c", @@ -152699,31 +168031,31 @@ "virology" ], "tools": [ - "samtools_view", - "fastp", "samtools_merge", - "ivar_consensus", - "split_file_to_collection", - "tp_sed_tool", - "EMBOSS: maskseq51", - "datamash_ops", - "samtools_stats", - "__ZIP_COLLECTION__", - "__FILTER_FAILED_DATASETS__", - "param_value_from_file", - "compose_text_param", - "__SORTLIST__", + "Cut1", + "tp_cat", + "Grep1", "__APPLY_RULES__", "qualimap_bamqc", - "__FLATTEN__", - "fasta_compute_length", - "ivar_trim", - "bwa_mem", "collection_element_identifiers", - "Cut1", + "param_value_from_file", + "EMBOSS: maskseq51", "multiqc", - "Grep1", - "tp_cat" + "__SORTLIST__", + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", + "fasta_compute_length", + "compose_text_param", + "ivar_consensus", + "__ZIP_COLLECTION__", + "samtools_stats", + "fastp", + "__FILTER_FAILED_DATASETS__", + "split_file_to_collection", + "tp_sed_tool", + "datamash_ops" ], "update_time": "2024-09-19", "versions": 1 @@ -152735,14 +168067,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "8d6d4f848067f3d9", @@ -152757,14 +168089,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152776,14 +168108,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "b7226d37b25df833", @@ -152798,14 +168130,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152817,14 +168149,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "9b18123afbe1264b", @@ -152839,14 +168171,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152858,14 +168190,14 @@ ], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", "Sequence trimming", - "RNA-Seq analysis", - "Sequencing quality control", "Sequence alignment", + "Transcriptome assembly", "Validation", - "Transcriptome assembly" + "Sequencing quality control", + "Primer removal", + "RNA-Seq analysis" ], "edam_topic": [], "id": "c2dee690320f9845", @@ -152880,14 +168212,14 @@ "rnaseq" ], "tools": [ - "rna_star", - "tp_awk_tool", - "multiqc", - "compose_text_param", "cufflinks", + "compose_text_param", + "multiqc", "map_param_value", + "rna_star", "stringtie", - "cutadapt" + "cutadapt", + "tp_awk_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152899,15 +168231,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "6efcacf14bfc18b3", @@ -152922,13 +168254,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152940,15 +168272,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "14b17f17d03c8424", @@ -152963,13 +168295,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -152981,15 +168313,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7a4ee63a04362967", @@ -153004,13 +168336,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -153022,15 +168354,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2617fee24459e680", @@ -153045,13 +168377,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-09-19", "versions": 1 @@ -153063,17 +168395,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "e0b89b4e50d1a99b", @@ -153088,15 +168420,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -153108,17 +168440,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2789fb3590727342", @@ -153133,15 +168465,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-09-19", "versions": 1 @@ -153168,8 +168500,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -153196,8 +168528,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-09-19", "versions": 1 @@ -153231,8 +168563,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "a804d976d351f2fc", @@ -153255,13 +168587,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "47cacc06d404a8c6", @@ -153275,9 +168607,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-09-05", "versions": 0 @@ -153287,14 +168619,14 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "d957bfeb3cd03db0", @@ -153307,11 +168639,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "merqury", "meryl", "quast", - "chromeister", "busco", - "merqury" + "chromeister" ], "update_time": "2024-09-02", "versions": 1 @@ -153321,14 +168653,14 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "d06665e4bc7fff6d", @@ -153341,11 +168673,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "merqury", "meryl", "quast", - "chromeister", "busco", - "merqury" + "chromeister" ], "update_time": "2024-09-02", "versions": 0 @@ -153355,14 +168687,14 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "478c79365fc9677f", @@ -153375,11 +168707,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "merqury", "meryl", "quast", - "chromeister", "busco", - "merqury" + "chromeister" ], "update_time": "2024-08-31", "versions": 0 @@ -153413,8 +168745,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "8ded019070c6687b", @@ -153437,13 +168769,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "178db14511c8f293", @@ -153457,9 +168789,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 0 @@ -153469,8 +168801,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "e7c5dfc703f66403", @@ -153565,8 +168897,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "5169ba49122ad39a", @@ -153613,8 +168945,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "3efbc617883dd1af", @@ -153661,13 +168993,13 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", + "Primer removal", "Sequencing quality control", "Box-Whisker plot plotting", - "Statistical calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", "Validation" ], @@ -153682,12 +169014,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqe", - "nanoplot", - "pycoqc", + "cutadapt", "multiqc", + "nanoplot", + "fastqe", "fastqc", - "cutadapt" + "pycoqc" ], "update_time": "2024-08-31", "versions": 1 @@ -153697,8 +169029,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "143d4cc586aff5a0", @@ -153745,13 +169077,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "43f2dabbc1932e30", @@ -153765,9 +169097,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 0 @@ -153777,8 +169109,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "f9719e48b907f35c", @@ -153801,8 +169133,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "b164468b137b73b9", @@ -153825,13 +169157,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "5d6773ed5b2f41cb", @@ -153845,9 +169177,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 2 @@ -153857,13 +169189,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "dd6f465ab1eb10b0", @@ -153877,9 +169209,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 1 @@ -153937,9 +169269,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "368f8ac35f4be589", @@ -153962,13 +169294,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "bd251174d94cde9d", @@ -153982,9 +169314,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 0 @@ -153994,13 +169326,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "115151c2c8998d44", @@ -154014,9 +169346,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 0 @@ -154026,8 +169358,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" + "Box-Whisker plot plotting", + "Scatter plot plotting" ], "edam_topic": [], "id": "4ff39e947c470103", @@ -154050,13 +169382,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "1f63ec596e578b1c", @@ -154070,9 +169402,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 0 @@ -154082,13 +169414,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "e08b04291839e79a", @@ -154102,9 +169434,9 @@ "tags": [], "tools": [ "fastqc", - "fastqe", + "cutadapt", "multiqc", - "cutadapt" + "fastqe" ], "update_time": "2024-08-31", "versions": 1 @@ -154114,14 +169446,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Visualisation", "Sequence contamination filtering", + "Sequence composition calculation", "Statistical calculation", - "Validation" + "Visualisation", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Formatting" ], "edam_topic": [], "id": "13ce18408ee7acc9", @@ -154134,11 +169466,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_star", - "pygenomeTracks", "fastp", "multiqc", - "fastqc" + "fastqc", + "rna_star", + "pygenomeTracks" ], "update_time": "2024-08-22", "versions": 12 @@ -154148,12 +169480,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "157e7614ae18849b", @@ -154166,23 +169498,23 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "gffcompare", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", - "filter_tabular", "sqlite_to_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "CONVERTER_gz_to_uncompressed", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "stringtie", + "hisat2", + "bed_to_protein_map" ], "update_time": "2024-08-12", "versions": 1 @@ -154206,13 +169538,13 @@ "tags": [], "tools": [ "arriba_get_filters", - "rna_star", - "tp_awk_tool", - "tab2fasta", "regex1", + "tab2fasta", "arriba", + "CONVERTER_gz_to_uncompressed", + "rna_star", "query_tabular", - "CONVERTER_gz_to_uncompressed" + "tp_awk_tool" ], "update_time": "2024-08-12", "versions": 0 @@ -154222,9 +169554,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "c622bd03677314aa", @@ -154237,18 +169569,18 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cshl_fastq_quality_filter", + "param_value_from_file", "Add_a_column1", "wc_gnu", - "Cut1", - "param_value_from_file", - "tp_grep_tool", - "pick_value", - "cshl_fastq_quality_filter", "compose_text_param", - "tp_text_file_with_recurring_lines", + "Cut1", + "map_param_value", "Convert characters1", + "tp_text_file_with_recurring_lines", "fastqc", - "map_param_value" + "tp_grep_tool", + "pick_value" ], "update_time": "2024-08-12", "versions": 100 @@ -154293,12 +169625,12 @@ "edam_operation": [ "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Visualisation", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", - "Mapping", + "Phylogenetic tree generation", "Multiple sequence alignment", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping", + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "eda40b58616a0fe4", @@ -154316,28 +169648,28 @@ "name:iwc" ], "tools": [ - "tp_multijoin_tool", - "bedtools_getfastabed", - "ggplot2_heatmap", - "regex1", - "Grouping1", - "clustalw", - "tp_split_on_column", "fasttree", - "__FILTER_FAILED_DATASETS__", "collapse_dataset", - "tab2fasta", - "newick_display", - "tp_replace_in_column", "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", + "collection_column_join", + "newick_display", "regexColumn1", - "Count1", - "Cut1", + "ggplot2_heatmap", + "regex1", + "tp_multijoin_tool", "__FILTER_EMPTY_DATASETS__", + "clustalw", + "fasta_merge_files_and_filter_unique_sequences", + "bedtools_getfastabed", + "Count1", + "tp_replace_in_column", "tp_sorted_uniq", + "tab2fasta", + "__FILTER_FAILED_DATASETS__", "Remove beginning1", - "collection_column_join" + "Grouping1", + "Cut1", + "tp_split_on_column" ], "update_time": "2024-07-03", "versions": 1 @@ -154360,8 +169692,8 @@ "pre-alphafold" ], "tools": [ - "cat1", - "fasplit" + "fasplit", + "cat1" ], "update_time": "2024-06-26", "versions": 12 @@ -154371,8 +169703,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequence analysis", "Sequencing quality control" ], @@ -154389,19 +169721,19 @@ "tools": [ "seq_filter_by_id", "obi_illumina_pairend", - "fastq_groomer", "obi_annotate", - "obi_ngsfilter", - "join1", - "Cut1", "obi_tab", "obi_stat", - "fastqc", - "ncbi_blastn_wrapper", "Filter1", - "obi_grep", + "ncbi_blastn_wrapper", + "obi_uniq", "obi_clean", - "obi_uniq" + "fastqc", + "join1", + "Cut1", + "obi_grep", + "obi_ngsfilter", + "fastq_groomer" ], "update_time": "2024-06-25", "versions": 0 @@ -154434,24 +169766,24 @@ "name:iwc" ], "tools": [ - "bcftools_norm", - "samtools_depth", - "table_compute", - "collapse_dataset", - "tp_cut_tool", - "Cut1", - "clair3", - "snpSift_extractFields", "bcftools_consensus", - "Count1", - "regexColumn1", - "minimap2", "Paste1", - "Remove beginning1", + "regexColumn1", + "snpSift_extractFields", + "bcftools_norm", "tp_head_tool", + "collapse_dataset", + "table_compute", + "samtools_depth", "samtools_coverage", + "Remove beginning1", + "snpSift_filter", + "Count1", + "clair3", "CONVERTER_gz_to_uncompressed", - "snpSift_filter" + "tp_cut_tool", + "minimap2", + "Cut1" ], "update_time": "2024-06-25", "versions": 1 @@ -154465,15 +169797,15 @@ ], "doi": "", "edam_operation": [ + "Genome assembly", + "Sequence assembly visualisation", + "Mapping assembly", + "Sequence assembly", "Base-calling", + "Cross-assembly", "De-novo assembly", - "Sequence assembly", "Variant calling", - "Sequence assembly visualisation", - "Antimicrobial resistance prediction", - "Genome assembly", - "Mapping assembly", - "Cross-assembly" + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "ef8c22c2525063a2", @@ -154491,18 +169823,18 @@ "name:microgalaxy" ], "tools": [ - "fasta2tab", - "abricate", - "flye", "collection_element_identifiers", - "tp_find_and_replace", - "bandage_image", + "flye", "param_value_from_file", "tab2fasta", - "medaka_consensus_pipeline", + "tp_find_and_replace", "compose_text_param", + "abricate", + "__BUILD_LIST__", + "fasta2tab", "split_file_to_collection", - "__BUILD_LIST__" + "bandage_image", + "medaka_consensus_pipeline" ], "update_time": "2024-06-25", "versions": 1 @@ -154516,9 +169848,9 @@ ], "doi": "", "edam_operation": [ - "Aggregation", "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Aggregation" ], "edam_topic": [], "id": "d9ba165e6ae55417", @@ -154536,8 +169868,8 @@ "name:iwc" ], "tools": [ - "taxonomy_krona_chart", "krakentools_kreport2krona", + "taxonomy_krona_chart", "kraken2" ], "update_time": "2024-06-25", @@ -154552,19 +169884,19 @@ ], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", + "Sequence contamination filtering", + "Visualisation", + "Statistical calculation", "Scatter plot plotting", - "Sequence alignment analysis", - "Sequence composition calculation", "Sequencing quality control", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Visualisation", - "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", - "Validation" + "Aggregation", + "Pairwise sequence alignment", + "Sequence composition calculation", + "Sequence alignment analysis", + "Validation", + "Data handling", + "Taxonomic classification" ], "edam_topic": [], "id": "25d52afddaa3451b", @@ -154583,23 +169915,23 @@ "name:iwc" ], "tools": [ + "regexColumn1", + "krakentools_extract_kraken_reads", "Add_a_column1", - "porechop", - "collapse_dataset", - "__FILTER_FAILED_DATASETS__", - "samtools_fastx", "kraken2", - "Cut1", - "nanoplot", - "krakentools_extract_kraken_reads", - "regexColumn1", - "minimap2", - "fastp", + "samtools_fastx", + "collapse_dataset", "multiqc", + "fastp", + "nanoplot", + "porechop", + "Grep1", + "__FILTER_FAILED_DATASETS__", "collection_column_join", "fastqc", - "Grep1", - "bamtools_split_mapped" + "bamtools_split_mapped", + "minimap2", + "Cut1" ], "update_time": "2024-06-25", "versions": 1 @@ -154609,8 +169941,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment" + "Sequence alignment", + "Data handling" ], "edam_topic": [], "id": "5aff01d0b5fabd84", @@ -154627,8 +169959,8 @@ ], "tools": [ "rna_star", - "fastq_dump", - "circexplorer" + "circexplorer", + "fastq_dump" ], "update_time": "2024-06-11", "versions": 5 @@ -154640,14 +169972,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "84c98a23187d2a36", @@ -154663,18 +169995,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-29", "versions": 0 @@ -154686,14 +170018,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "39b464084d930a33", @@ -154710,18 +170042,18 @@ "cloud-costs" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-28", "versions": 0 @@ -154733,14 +170065,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "3f39cf407c185724", @@ -154757,18 +170089,18 @@ "cloud-costs" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2024-05-28", "versions": 0 @@ -154780,15 +170112,15 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequencing quality control", + "Mapping", "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "5cd9b9338e75f254", @@ -154803,18 +170135,18 @@ "rnaseq" ], "tools": [ - "bedtools_genomecoveragebed", - "rna_star", - "tp_awk_tool", - "revertR2orientationInBam", - "param_value_from_file", "wig_to_bigWig", - "multiqc", - "compose_text_param", + "param_value_from_file", "cufflinks", - "map_param_value", + "compose_text_param", + "multiqc", "bamFilter", - "cutadapt" + "map_param_value", + "revertR2orientationInBam", + "rna_star", + "cutadapt", + "bedtools_genomecoveragebed", + "tp_awk_tool" ], "update_time": "2024-05-28", "versions": 0 @@ -154824,18 +170156,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "69233fb6edfcdde9", @@ -154848,15 +170180,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-05-20", "versions": 1 @@ -154866,18 +170198,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "8b8a5b50f2edc72c", @@ -154890,14 +170222,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "featurecounts", "Filter1", - "hisat2", - "deg_annotate", + "featurecounts", + "cutadapt", "multiqc", - "deseq2", - "cutadapt" + "deg_annotate", + "fastqc", + "hisat2", + "deseq2" ], "update_time": "2024-05-20", "versions": 2 @@ -154907,18 +170239,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "4f2818b6620037af", @@ -154931,15 +170263,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", "sort1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-05-18", "versions": 0 @@ -154949,14 +170281,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Sequence alignment", + "RNA-Seq quantification", "Read summarisation", - "Sequence contamination filtering", - "Statistical calculation", - "RNA-Seq quantification" + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "811bbada546850bd", @@ -154969,13 +170301,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "fastq_dump", - "featurecounts", "samtools_stats", + "featurecounts", + "trimmomatic", "fastp", + "fastqc", "hisat2", - "fastqc" + "fastq_dump" ], "update_time": "2024-05-08", "versions": 1 @@ -154985,18 +170317,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c3e198bc2146b4ad", @@ -155009,15 +170341,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-05-03", "versions": 0 @@ -155027,18 +170359,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a9fa6101f1fb13e2", @@ -155052,12 +170384,12 @@ "tags": [], "tools": [ "featurecounts", - "hisat2", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-30", "versions": 1 @@ -155067,18 +170399,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "d5ecfdbc04b24227", @@ -155091,14 +170423,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-30", "versions": 2 @@ -155108,18 +170440,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "525612313de7591e", @@ -155132,14 +170464,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-30", "versions": 0 @@ -155149,18 +170481,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "f268c181a47d0cab", @@ -155174,14 +170506,14 @@ "tags": [], "tools": [ "cat1", - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-19", "versions": 0 @@ -155191,18 +170523,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "79522a1f7b0c53cb", @@ -155216,14 +170548,14 @@ "tags": [], "tools": [ "cat1", - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-18", "versions": 0 @@ -155250,8 +170582,8 @@ "tags": [], "tools": [ "split_file_to_collection", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-18", "versions": 1 @@ -155261,14 +170593,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Statistical calculation", - "Sequence composition calculation", - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "d8a4a8bc4fa2f9ee", @@ -155281,14 +170613,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", + "ivar_trim", "samtools_sort", - "jbrowse", "ivar_consensus", - "fastqc", "ivar_variants", - "ivar_trim" + "bwa_mem", + "fastqc", + "jbrowse", + "samtools_flagstat" ], "update_time": "2024-04-16", "versions": 1 @@ -155298,13 +170630,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Read mapping", - "Genome indexing", + "Statistical calculation", "Generation", + "Genome indexing", + "Sequence alignment", "Sequencing quality control", - "Sequence alignment" + "Read mapping" ], "edam_topic": [], "id": "f52fb12383c8a214", @@ -155317,13 +170649,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", + "fastqc", "samtools_sort", "ivar_consensus", - "fastqc", "ivar_variants", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "samtools_flagstat" ], "update_time": "2024-04-16", "versions": 10 @@ -155333,18 +170665,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "2f7c0e3221cbca2f", @@ -155357,14 +170689,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-12", "versions": 1 @@ -155374,18 +170706,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "f0ced9a5d34b2aff", @@ -155398,14 +170730,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-12", "versions": 0 @@ -155415,18 +170747,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "b6db525b1b73394b", @@ -155439,14 +170771,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155456,18 +170788,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "97628b0604d5ec77", @@ -155480,14 +170812,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 1 @@ -155497,18 +170829,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "95a9070469a895c3", @@ -155521,14 +170853,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155538,18 +170870,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "4f562265cbb14cd6", @@ -155562,14 +170894,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155579,18 +170911,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5ea74382fb77eb10", @@ -155603,15 +170935,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155621,18 +170953,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "ad13b4a61e8987b1", @@ -155645,14 +170977,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 1 @@ -155662,15 +170994,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "e8d3651c07ce0bec", @@ -155687,13 +171019,13 @@ "encff821rsh" ], "tools": [ - "trimmomatic", - "featurecounts", "Filter1", + "featurecounts", + "trimmomatic", "multiqc", - "hisat2", "deg_annotate", "fastqc", + "hisat2", "deseq2" ], "update_time": "2024-04-11", @@ -155704,18 +171036,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "6469ade8f6f7c718", @@ -155728,14 +171060,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 1 @@ -155745,12 +171077,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Sequence assembly visualisation", + "Genome assembly", "Scatter plot plotting", "Antimicrobial resistance prediction", - "Genome assembly", "Box-Whisker plot plotting", - "Sequence assembly visualisation" + "Aggregation" ], "edam_topic": [], "id": "c9b7de574fb2f2d5", @@ -155764,10 +171096,10 @@ "tags": [], "tools": [ "abricate", - "bandage_image", "nanoplot", - "staramr_search", - "unicycler" + "bandage_image", + "unicycler", + "staramr_search" ], "update_time": "2024-04-11", "versions": 0 @@ -155777,18 +171109,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "31449596b22f81f4", @@ -155801,14 +171133,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155818,18 +171150,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "4efed79608f85604", @@ -155842,14 +171174,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 1 @@ -155859,18 +171191,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "7c866ed4a3552d0d", @@ -155883,14 +171215,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155900,18 +171232,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "e52a3479c8216291", @@ -155924,14 +171256,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -155941,16 +171273,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Validation" ], "edam_topic": [], "id": "8d6010d07cc2e170", @@ -155964,10 +171296,10 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2024-04-11", "versions": 2 @@ -155977,8 +171309,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "d5717afa6cce6fb4", @@ -155992,9 +171324,9 @@ "tags": [], "tools": [ "tp_sort_header_tool", - "deseq2", "Filter1", - "deg_annotate" + "deg_annotate", + "deseq2" ], "update_time": "2024-04-11", "versions": 2 @@ -156004,18 +171336,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "91cfd96f697ba034", @@ -156028,14 +171360,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 0 @@ -156045,18 +171377,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "046a1c600a6b77c2", @@ -156070,11 +171402,11 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 1 @@ -156084,8 +171416,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "84a8eb379440656e", @@ -156098,11 +171430,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "ggplot2_heatmap2", - "join1", - "Cut1", "Filter1", "deg_annotate", + "join1", + "Cut1", + "ggplot2_heatmap2", "deseq2" ], "update_time": "2024-04-11", @@ -156113,16 +171445,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Validation" ], "edam_topic": [], "id": "723513b09d6690b8", @@ -156136,10 +171468,10 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2024-04-11", "versions": 1 @@ -156149,18 +171481,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "fd477917a3d27f61", @@ -156174,11 +171506,11 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-11", "versions": 3 @@ -156194,11 +171526,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "281ea78467e73147", @@ -156243,8 +171575,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-04-11", "versions": 1 @@ -156254,18 +171586,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "9ec9fe2715d7cfdc", @@ -156278,15 +171610,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156296,18 +171628,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a7346c25dfdf2e3e", @@ -156320,15 +171652,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156338,18 +171670,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "9e8d9b7055b7c863", @@ -156362,15 +171694,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "tabular_to_csv", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156380,18 +171712,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "cb960edf95d2dc35", @@ -156404,13 +171736,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156420,8 +171752,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "721e528c2ae6d8ee", @@ -156434,9 +171766,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "deseq2", "Filter1", - "deg_annotate" + "deg_annotate", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156446,10 +171778,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Read summarisation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control", + "Read summarisation" ], "edam_topic": [], "id": "9157a7438977b9e9", @@ -156474,12 +171806,12 @@ "doi": "", "edam_operation": [ "Statistical calculation", - "Sequence composition calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Sequencing quality control", - "Sequence alignment", "Validation" ], "edam_topic": [], @@ -156493,10 +171825,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", "hisat2", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2024-04-10", "versions": 0 @@ -156507,12 +171839,12 @@ "doi": "", "edam_operation": [ "Statistical calculation", - "Sequence composition calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Sequencing quality control", - "Sequence alignment", "Validation" ], "edam_topic": [], @@ -156526,10 +171858,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "multiqc", - "fastqc", "hisat2", - "cutadapt" + "cutadapt", + "multiqc", + "fastqc" ], "update_time": "2024-04-10", "versions": 0 @@ -156539,18 +171871,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "4e096a68187ce652", @@ -156563,14 +171895,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-10", "versions": 0 @@ -156580,18 +171912,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "2999a1891ffe201b", @@ -156604,14 +171936,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-09", "versions": 0 @@ -156621,18 +171953,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c296b3848708f6f1", @@ -156645,14 +171977,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-09", "versions": 0 @@ -156662,18 +171994,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "05b17b9d70c1db8b", @@ -156686,14 +172018,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-09", "versions": 0 @@ -156703,18 +172035,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "1c886f008a36b0b8", @@ -156727,14 +172059,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-09", "versions": 0 @@ -156744,18 +172076,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "bda98c5a0ea70dd0", @@ -156768,16 +172100,16 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_cat", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt", - "tp_cat" + "hisat2", + "deseq2" ], "update_time": "2024-04-08", "versions": 0 @@ -156787,18 +172119,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "6f0801fecbba5d3f", @@ -156811,16 +172143,16 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "rna_star", - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "hisat2", + "deseq2" ], "update_time": "2024-04-08", "versions": 0 @@ -156830,18 +172162,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "7becafd394472dfb", @@ -156854,12 +172186,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_star", "featurecounts", "multiqc", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "deseq2" ], "update_time": "2024-04-08", "versions": 29 @@ -156869,18 +172201,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "410d0d19b6589c78", @@ -156893,14 +172225,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-08", "versions": 0 @@ -156910,18 +172242,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c65a5af6c0383f8c", @@ -156934,14 +172266,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-07", "versions": 1 @@ -156951,18 +172283,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "af990cca72794142", @@ -156975,14 +172307,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-07", "versions": 0 @@ -156992,18 +172324,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "8483ae422665a6c1", @@ -157016,14 +172348,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-07", "versions": 0 @@ -157033,18 +172365,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "6204bbcfe56931eb", @@ -157057,14 +172389,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-05", "versions": 0 @@ -157074,18 +172406,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "383ce49fa7a367e9", @@ -157098,15 +172430,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-03", "versions": 0 @@ -157116,18 +172448,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5314a7a4732a0ef1", @@ -157140,15 +172472,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-02", "versions": 0 @@ -157158,18 +172490,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "20e5e6b233ffb951", @@ -157182,15 +172514,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-02", "versions": 0 @@ -157200,18 +172532,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "6cdbcd1f667d0f16", @@ -157224,15 +172556,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-04-01", "versions": 0 @@ -157242,18 +172574,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "ff42213dda7d3e59", @@ -157267,14 +172599,14 @@ "tags": [], "tools": [ "cat1", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-31", "versions": 40 @@ -157284,18 +172616,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "73ff1aa9acc0ad2a", @@ -157308,13 +172640,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-30", "versions": 1 @@ -157324,18 +172656,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5a4e49ef8693d7c4", @@ -157348,15 +172680,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-30", "versions": 0 @@ -157366,18 +172698,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "aaaf580eb00459b6", @@ -157390,15 +172722,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-30", "versions": 0 @@ -157408,10 +172740,10 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis", + "RNA-Seq quantification", "Read summarisation", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "66b5c7dd3e58193f", @@ -157425,9 +172757,9 @@ "tags": [], "tools": [ "deseq2", - "featurecounts", "Filter1", - "deg_annotate" + "deg_annotate", + "featurecounts" ], "update_time": "2024-03-28", "versions": 0 @@ -157439,13 +172771,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "1ad4c47cee851dda", @@ -157458,10 +172790,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-03-28", "versions": 1 @@ -157474,13 +172806,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -157496,19 +172828,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2024-03-28", "versions": 1 @@ -157520,17 +172852,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "fa4fa7353dffef9a", @@ -157545,15 +172877,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2024-03-28", "versions": 1 @@ -157566,11 +172898,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "6a04c54236f30e8d", @@ -157586,15 +172918,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-03-28", "versions": 1 @@ -157604,18 +172936,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "608f3ad8f485e7a8", @@ -157628,15 +172960,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", - "__TAG_FROM_FILE__", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "__TAG_FROM_FILE__", + "hisat2", + "deseq2" ], "update_time": "2024-03-27", "versions": 0 @@ -157646,18 +172978,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "db0bc7357c181222", @@ -157671,13 +173003,13 @@ "tags": [], "tools": [ "featurecounts", - "__TAG_FROM_FILE__", - "hisat2", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "__TAG_FROM_FILE__", + "hisat2", + "deseq2" ], "update_time": "2024-03-27", "versions": 0 @@ -157687,18 +173019,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "02b8d033d9b1fa05", @@ -157711,15 +173043,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "tabular_to_csv", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-25", "versions": 0 @@ -157729,18 +173061,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "925c167abd5610ae", @@ -157753,13 +173085,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-24", "versions": 0 @@ -157769,18 +173101,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a7d1cf2bb636e695", @@ -157793,14 +173125,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-21", "versions": 0 @@ -157810,18 +173142,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "8483e8d3e8d0ddc9", @@ -157834,14 +173166,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2024-03-21", "versions": 0 @@ -157854,8 +173186,8 @@ ], "doi": "", "edam_operation": [ - "Variant calling", - "DNA barcoding" + "DNA barcoding", + "Variant calling" ], "edam_topic": [], "id": "400fbd96fb04c60e", @@ -157870,17 +173202,17 @@ "name:amplicon" ], "tools": [ - "dada2_plotQualityProfile", "dada2_makeSequenceTable", + "dada2_assignTaxonomyAddspecies", + "dada2_plotQualityProfile", + "dada2_dada", + "dada2_removeBimeraDenovo", "dada2_seqCounts", - "dada2_mergePairs", "dada2_filterAndTrim", - "__UNZIP_COLLECTION__", "dada2_learnErrors", - "dada2_dada", + "dada2_mergePairs", "__APPLY_RULES__", - "dada2_removeBimeraDenovo", - "dada2_assignTaxonomyAddspecies" + "__UNZIP_COLLECTION__" ], "update_time": "2024-03-21", "versions": 1 @@ -157909,14 +173241,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2024-03-21", "versions": 1 @@ -157928,15 +173260,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "2543e425fa6d5144", @@ -157951,13 +173283,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -157969,15 +173301,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "4bd6c5c12fb1a69a", @@ -157992,13 +173324,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -158010,15 +173342,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e57c6d05b560e206", @@ -158033,13 +173365,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2024-03-21", "versions": 1 @@ -158067,8 +173399,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-03-21", "versions": 1 @@ -158096,8 +173428,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2024-03-14", "versions": 1 @@ -158107,9 +173439,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Scatter plot plotting", "Sequencing quality control", "Box-Whisker plot plotting" ], @@ -158124,8 +173456,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "nanoplot" + "nanoplot", + "fastqc" ], "update_time": "2024-03-08", "versions": 0 @@ -158135,8 +173467,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", "Sequencing quality control" ], "edam_topic": [], @@ -158150,8 +173482,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "pycoqc" + "pycoqc", + "fastqc" ], "update_time": "2024-03-08", "versions": 0 @@ -158164,16 +173496,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "79bf7b0f5e9052d7", @@ -158188,17 +173520,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-03-07", "versions": 1 @@ -158214,11 +173546,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "c64dcc1e6a67f3e4", @@ -158248,8 +173580,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "73565f6cb4136370", @@ -158264,11 +173596,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2024-03-07", "versions": 1 @@ -158281,16 +173613,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "ecfb8a08e5a40e15", @@ -158306,16 +173638,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-03-07", "versions": 1 @@ -158343,17 +173675,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2024-03-07", "versions": 1 @@ -158379,20 +173711,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2024-03-07", "versions": 1 @@ -158404,14 +173736,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "888eb87b62c4e6dd", @@ -158428,26 +173760,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2024-03-07", "versions": 1 @@ -158488,16 +173820,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1905ec04d5841f09", @@ -158513,16 +173845,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2024-02-22", "versions": 1 @@ -158534,13 +173866,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", + "Sequence assembly visualisation", "Mapping assembly", - "Cross-assembly", - "Sequence assembly visualisation" + "Cross-assembly" ], "edam_topic": [], "id": "d832905fbaf2ca31", @@ -158553,10 +173885,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fasta-stats", "bandage_image", - "quast", - "flye" + "fasta-stats", + "flye", + "quast" ], "update_time": "2024-02-15", "versions": 1 @@ -158569,16 +173901,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "4ebf1297793870e7", @@ -158593,17 +173925,17 @@ "vgp_curated" ], "tools": [ - "tp_easyjoin_tool", - "Add_a_column1", - "tp_awk_tool", - "Cut1", "param_value_from_file", + "Add_a_column1", + "merqury", "tp_grep_tool", + "gfastats", + "busco", + "tp_easyjoin_tool", "minimap2", - "merqury", + "Cut1", "purge_dups", - "busco", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-02-15", "versions": 1 @@ -158619,11 +173951,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "3fd10af90a07f771", @@ -158650,14 +173982,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", + "Genome assembly", "Scatter plot plotting", + "Sequence assembly visualisation", "Mapping assembly", - "De-novo assembly", - "Pairwise sequence alignment", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome assembly", + "Aggregation", + "Pairwise sequence alignment", + "De-novo assembly", "Sequence analysis" ], "edam_topic": [], @@ -158671,15 +174003,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "miniasm", + "racon", + "PlasFlow", + "nanoplot", "gfa_to_fa", "bandage_image", - "nanoplot", - "racon", + "unicycler", "minimap2", - "PlasFlow", - "miniasm", - "staramr_search", - "unicycler" + "staramr_search" ], "update_time": "2024-02-03", "versions": 0 @@ -158692,18 +174024,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "b1f45d2f8d8343e9", @@ -158719,19 +174051,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2024-01-18", "versions": 1 @@ -158743,18 +174075,18 @@ ], "doi": "", "edam_operation": [ - "Validation", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", + "Tree-based sequence alignment", + "Methylation analysis", + "Generation", + "Genome indexing", "Variant calling", - "Sequence alignment", + "Validation", + "Read mapping", "Variant classification", - "SNP detection", - "Sequence contamination filtering", - "Genome indexing", - "Methylation analysis", - "Tree-based sequence alignment" + "SNP detection" ], "edam_topic": [], "id": "7563b3ef697a69fd", @@ -158771,21 +174103,21 @@ "iwc" ], "tools": [ - "pangolin", - "bwa_mem", - "nextclade", - "snpeff_sars_cov_2", - "samtools_view", - "tp_sed_tool", "samtools_stats", - "fastp", + "nextclade", "ivar_consensus", + "fastp", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_variants", + "tp_cat", + "tp_sed_tool", + "bwa_mem", "ivar_trim", - "tp_cat" + "__FLATTEN__", + "snpeff_sars_cov_2", + "pangolin", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2024-01-18", "versions": 1 @@ -158798,11 +174130,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "41bd0340dcde60ec", @@ -158818,15 +174150,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2024-01-18", "versions": 1 @@ -158842,11 +174174,11 @@ ], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "644d8e4c78df8e36", @@ -158892,14 +174224,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-12-21", "versions": 1 @@ -158928,14 +174260,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-12-21", "versions": 1 @@ -158945,30 +174277,30 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequencing quality control", - "Differential gene expression analysis", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Fold recognition", - "Antimicrobial resistance prediction", + "Genome annotation", "Homology-based gene prediction", - "Query and retrieval", - "Genome assembly", - "Sequence clustering", - "Scaffolding", + "Information extraction", + "Sequence motif recognition", "Mapping assembly", + "Fold recognition", + "Scaffolding", + "Sequencing quality control", "Cross-assembly", + "Box-Whisker plot plotting", + "Transcriptome assembly", + "Coding region prediction", "Protein feature detection", - "Filtering", - "Scatter plot plotting", "Sequence assembly validation", - "Genome annotation", - "Sequence motif recognition", "Gene prediction", - "Coding region prediction", - "Information extraction", - "Transcriptome assembly" + "Sequence clustering", + "Genome assembly", + "Differential gene expression analysis", + "Scatter plot plotting", + "Sequence assembly visualisation", + "Query and retrieval", + "De-novo assembly", + "Filtering", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "35f39173f0ac9179", @@ -158987,16 +174319,16 @@ "annotation" ], "tools": [ - "interproscan", - "abricate", + "prokka", "flye", - "filtlong", - "bandage_image", + "abricate", + "antismash", "nanoplot", "eggnog_mapper", - "antismash", + "bandage_image", "busco", - "prokka", + "interproscan", + "filtlong", "staramr_search" ], "update_time": "2023-12-20", @@ -159011,20 +174343,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d9c181fd954b629a", @@ -159040,22 +174372,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159069,20 +174401,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "08fac3b4c128e597", @@ -159098,22 +174430,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159127,20 +174459,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Sequencing quality control", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", + "Sequencing quality control", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d42d7b1aa47e870f", @@ -159156,22 +174488,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", "Cut1", - "bandage_image", - "param_value_from_file", "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", + "bandage_image", "merqury", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159184,16 +174516,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "ac8bdc5a0b2d70cd", @@ -159209,16 +174541,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159231,16 +174563,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "0c11e1ba5e8fa21b", @@ -159256,16 +174588,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159278,16 +174610,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "a1015b83baa0eb6d", @@ -159303,16 +174635,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-12-14", "versions": 1 @@ -159325,13 +174657,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -159347,19 +174679,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-12-14", "versions": 1 @@ -159372,13 +174704,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -159394,19 +174726,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-12-14", "versions": 1 @@ -159419,13 +174751,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -159441,19 +174773,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-12-14", "versions": 1 @@ -159479,18 +174811,18 @@ "generic" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2023-12-07", "versions": 1 @@ -159503,18 +174835,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "0cc8c8875df6bccb", @@ -159530,19 +174862,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-12-07", "versions": 1 @@ -159569,8 +174901,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-12-07", "versions": 1 @@ -159597,8 +174929,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-12-07", "versions": 1 @@ -159610,17 +174942,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a5ccbb9aced9ac53", @@ -159635,15 +174967,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-12-07", "versions": 1 @@ -159655,14 +174987,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "8b955274ca3ca3dc", @@ -159678,18 +175010,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-12-07", "versions": 1 @@ -159717,8 +175049,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-12-07", "versions": 1 @@ -159746,8 +175078,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-12-07", "versions": 1 @@ -159775,17 +175107,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2023-12-07", "versions": 1 @@ -159811,20 +175143,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2023-12-07", "versions": 1 @@ -159836,15 +175168,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "ae894cff1d1aba01", @@ -159862,17 +175194,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-12-07", "versions": 1 @@ -159884,17 +175216,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "b20f28151e46d3e0", @@ -159909,15 +175241,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -159929,14 +175261,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "25403321a649a92b", @@ -159952,18 +175284,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -159991,8 +175323,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-30", "versions": 1 @@ -160020,8 +175352,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-30", "versions": 1 @@ -160049,17 +175381,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2023-11-30", "versions": 1 @@ -160085,20 +175417,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2023-11-30", "versions": 1 @@ -160110,15 +175442,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "3c7b55daae7c119b", @@ -160136,17 +175468,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2023-11-30", "versions": 1 @@ -160173,8 +175505,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-23", "versions": 1 @@ -160202,8 +175534,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-11-23", "versions": 1 @@ -160232,14 +175564,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-16", "versions": 1 @@ -160252,8 +175584,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "11f1564f2bd815d8", @@ -160268,11 +175600,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-16", "versions": 1 @@ -160301,14 +175633,14 @@ ], "tools": [ "kraken2", - "parse_mito_blast", - "gfastats", + "ncbi_blastn_wrapper", "tp_find_and_replace", - "tp_grep_tool", + "tp_cat", + "gfastats", "tp_sed_tool", - "ncbi_blastn_wrapper", - "ncbi_dustmasker_wrapper", - "tp_cat" + "parse_mito_blast", + "tp_grep_tool", + "ncbi_dustmasker_wrapper" ], "update_time": "2023-11-13", "versions": 1 @@ -160322,20 +175654,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "a02c102e179596cb", @@ -160351,22 +175683,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160380,20 +175712,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fff2e49bc90e38ca", @@ -160409,22 +175741,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160438,20 +175770,20 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", + "Sequence assembly visualisation", + "Primer removal", "Sequencing quality control", "Phasing", - "k-mer counting", - "Sequence assembly visualisation", - "Sequence assembly validation", "Scaffolding", - "Primer removal", + "Transcriptome assembly", + "k-mer counting", "Read pre-processing", - "Genome assembly", + "De-novo assembly", "Sequence trimming", + "Sequence assembly validation", "Validation", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "f7a866159f1eaecf", @@ -160467,22 +175799,22 @@ "reviewed" ], "tools": [ + "Paste1", + "param_value_from_file", "Add_a_column1", - "tp_awk_tool", + "cutadapt", "Cut1", - "bandage_image", - "param_value_from_file", - "tp_grep_tool", + "multiqc", "tp_replace_in_line", - "tp_sed_tool", - "Paste1", + "gfastats", "merqury", + "bandage_image", "Convert characters1", + "tp_sed_tool", "busco", - "multiqc", - "cutadapt", + "tp_grep_tool", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160495,18 +175827,18 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Phasing", - "k-mer counting", + "Genome assembly", "Sequence assembly visualisation", - "Sequence assembly validation", + "Phasing", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "e031af90daa2cadf", @@ -160522,19 +175854,19 @@ "reviewed" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "bandage_image", "param_value_from_file", + "merqury", "tp_grep_tool", "tp_replace_in_line", - "merqury", + "gfastats", + "Cut1", + "bandage_image", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160547,8 +175879,8 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation" + "Visualisation", + "Data handling" ], "edam_topic": [], "id": "bcb0be4f4a0e369f", @@ -160563,11 +175895,11 @@ "vgp_curated" ], "tools": [ - "ggplot2_point", - "bionano_scaffold", - "Cut1", "param_value_from_file", - "gfastats" + "gfastats", + "bionano_scaffold", + "ggplot2_point", + "Cut1" ], "update_time": "2023-11-13", "versions": 1 @@ -160594,8 +175926,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -160622,8 +175954,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -160650,8 +175982,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -160678,8 +176010,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -160706,8 +176038,8 @@ "vgp" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2023-11-13", "versions": 1 @@ -160720,16 +176052,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "d83d5ecf31c20490", @@ -160745,16 +176077,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160767,16 +176099,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "fea0e6c02c2f6274", @@ -160792,16 +176124,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160814,16 +176146,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "40740c32b9a550c9", @@ -160839,16 +176171,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160861,16 +176193,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1ce2a725df3adb74", @@ -160886,16 +176218,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -160908,13 +176240,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -160930,19 +176262,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-13", "versions": 1 @@ -160955,13 +176287,13 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", - "Data handling", "Genome assembly", - "Mapping", "Sequence alignment", + "Data handling", + "Sequence assembly validation", + "Scaffolding", + "Mapping", "Transcriptome assembly" ], "edam_topic": [], @@ -160977,19 +176309,19 @@ "vgp_curated" ], "tools": [ - "bellerophon", + "bwa_mem2", + "param_value_from_file", "__EXTRACT_DATASET__", + "yahs", + "gfastats", + "pretext_snapshot", + "tp_sort_header_tool", "bedtools_bamtobed", + "busco", "ggplot2_point", "pretext_map", "Cut1", - "tp_sort_header_tool", - "param_value_from_file", - "yahs", - "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "bellerophon" ], "update_time": "2023-11-13", "versions": 1 @@ -161001,15 +176333,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7c2e7b292803b3e9", @@ -161024,13 +176356,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -161042,15 +176374,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9bc31dff5bcec42b", @@ -161065,13 +176397,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-11-13", "versions": 1 @@ -161083,17 +176415,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "c87c1f8c4eff415a", @@ -161108,15 +176440,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-13", "versions": 1 @@ -161128,17 +176460,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "0f7406ada6706c91", @@ -161153,15 +176485,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-11-13", "versions": 1 @@ -161172,8 +176504,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree analysis", - "Nucleic acid sequence analysis", - "Visualisation" + "Visualisation", + "Nucleic acid sequence analysis" ], "edam_topic": [], "id": "6b7e565258a9da2a", @@ -161190,14 +176522,14 @@ "shotgun" ], "tools": [ - "metaphlan2krona", - "metaphlan2", - "Cut1", - "taxonomy_krona_chart", "humann2_renorm_table", - "humann2", + "taxonomy_krona_chart", "humann2_regroup_table", - "merge_metaphlan_tables" + "merge_metaphlan_tables", + "metaphlan2", + "metaphlan2krona", + "humann2", + "Cut1" ], "update_time": "2023-10-26", "versions": 125 @@ -161225,8 +176557,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-10-05", "versions": 1 @@ -161252,8 +176584,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "repeatmasker_wrapper", - "repeatmodeler" + "repeatmodeler", + "repeatmasker_wrapper" ], "update_time": "2023-09-28", "versions": 1 @@ -161263,15 +176595,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "cef4a514f35576e5", @@ -161285,12 +176617,12 @@ "tags": [], "tools": [ "bowtie2", - "trimmomatic", "featurecounts", + "trimmomatic", "multiqc", + "__FLATTEN__", "fastqc", - "deseq2", - "__FLATTEN__" + "deseq2" ], "update_time": "2023-09-20", "versions": 13 @@ -161346,8 +176678,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-09-14", "versions": 1 @@ -161359,15 +176691,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b8968fb0bf796e53", @@ -161382,13 +176714,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -161400,15 +176732,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "48a25f8e58d068e6", @@ -161423,13 +176755,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-09-07", "versions": 1 @@ -161441,17 +176773,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2f520cb446adf726", @@ -161466,15 +176798,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-09-07", "versions": 1 @@ -161502,8 +176834,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2023-09-07", "versions": 1 @@ -161515,15 +176847,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "1ff259845498b818", @@ -161538,13 +176870,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-08-31", "versions": 1 @@ -161556,15 +176888,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "8433a2f79b2e5894", @@ -161579,13 +176911,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-08-31", "versions": 1 @@ -161606,8 +176938,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "tp_cat" ], "update_time": "2023-07-10", @@ -161622,13 +176954,13 @@ ], "doi": "", "edam_operation": [ - "Read summarisation", "Sequence contamination filtering", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Validation", - "RNA-Seq quantification" + "Sequence alignment", + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Formatting" ], "edam_topic": [], "id": "49b5c35b9723fa62", @@ -161646,14 +176978,14 @@ "bwa-mem2" ], "tools": [ + "bwa_mem2", "cat1", - "picard_MarkDuplicates", "featurecounts", + "qualimap_bamqc", "fastp", - "bwa_mem2", + "picard_AddOrReplaceReadGroups", "multiqc", - "qualimap_bamqc", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2023-06-27", "versions": 12 @@ -161665,19 +176997,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Protein sequence analysis", - "Sequence alignment", - "Sequence comparison", "Sequence contamination filtering", "Statistical calculation", - "RNA-Seq analysis", + "Sequence alignment", + "Sequencing quality control", + "Sequence annotation", + "Sequence comparison", + "Transcriptome assembly", + "Sequence composition calculation", + "Protein sequence analysis", "Sequence analysis", "Validation", - "Transcriptome assembly" + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6e1e24f9e0326930", @@ -161693,33 +177025,33 @@ "name:isoform-switching" ], "tools": [ - "isoformswitchanalyzer", - "rseqc_read_distribution", - "__FILTER_FROM_FILE__", + "rseqc_junction_annotation", + "rseqc_geneBody_coverage", + "tp_cat", + "fastqc", + "rna_star", "tp_grep_tool", "rseqc_infer_experiment", - "fastp", - "fastqc", - "rseqc_junction_saturation", - "pfamscan", - "gffread", - "stringtie_merge", - "sort1", - "rseqc_inner_distance", "param_value_from_file", - "gtftobed12", - "stringtie", + "sort1", + "multiqc", "__FLATTEN__", - "rseqc_junction_annotation", "cpat", - "tp_awk_tool", - "Cut1", - "rna_star", + "stringtie", + "gffread", + "rseqc_junction_saturation", "tp_sorted_uniq", + "rseqc_inner_distance", + "rseqc_read_distribution", + "isoformswitchanalyzer", + "stringtie_merge", + "fastp", + "gtftobed12", "Remove beginning1", - "rseqc_geneBody_coverage", - "multiqc", - "tp_cat" + "Cut1", + "__FILTER_FROM_FILE__", + "tp_awk_tool", + "pfamscan" ], "update_time": "2023-06-12", "versions": 4 @@ -161729,16 +177061,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Statistical calculation", + "Phylogenetic tree generation", "Sequencing quality control", + "Sequence composition calculation", "Variant calling", - "Phylogenetic tree generation", + "Validation", + "Phylogenetic tree visualisation", "Genome visualisation", "Antimicrobial resistance prediction", - "Statistical calculation", - "Taxonomic classification", - "Phylogenetic tree visualisation", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "a61d4bda54de7cd1", @@ -161755,15 +177087,15 @@ "galaxy-training-network" ], "tools": [ - "tb_profiler_profile", - "tbvcfreport", "kraken2", "trimmomatic", + "multiqc", "tb_variant_filter", + "tbvcfreport", + "fastqc", "snippy", - "multiqc", "jbrowse", - "fastqc" + "tb_profiler_profile" ], "update_time": "2023-06-12", "versions": 0 @@ -161776,17 +177108,17 @@ ], "doi": "", "edam_operation": [ - "Sequence annotation", - "Ab-initio gene prediction", - "Genome visualisation", - "Sequence assembly validation", - "Genome annotation", "Gene prediction", + "Genome annotation", "Homology-based gene prediction", - "Scaffolding", "Genome assembly", + "Scaffolding", + "Transcriptome assembly", "Operation", - "Transcriptome assembly" + "Sequence assembly validation", + "Ab-initio gene prediction", + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "7e40485d1ed45b7c", @@ -161801,15 +177133,15 @@ "genome-annotation" ], "tools": [ - "maker_map_ids", "jcvi_gff_stats", "gffread", - "maker", - "augustus_training", "fasta-stats", + "snap_training", "busco", + "maker_map_ids", + "maker", "jbrowse", - "snap_training" + "augustus_training" ], "update_time": "2023-06-02", "versions": 3 @@ -161821,18 +177153,18 @@ ], "doi": "", "edam_operation": [ - "Sequence annotation", + "Genome annotation", + "Homology-based gene prediction", + "Information extraction", "Genome assembly", "Sequence alignment", "Fold recognition", - "Genome visualisation", - "Genome annotation", - "Homology-based gene prediction", + "Scaffolding", "Query and retrieval", + "Transcriptome assembly", "Sequence assembly validation", - "Scaffolding", - "Information extraction", - "Transcriptome assembly" + "Genome visualisation", + "Sequence annotation" ], "edam_topic": [], "id": "4e161a8f5098cc49", @@ -161847,13 +177179,13 @@ "genome-annotation" ], "tools": [ - "funannotate_annotate", "aegean_parseval", - "rna_star", "eggnog_mapper", - "jbrowse", "busco", + "rna_star", "funannotate_compare", + "jbrowse", + "funannotate_annotate", "funannotate_predict" ], "update_time": "2023-06-02", @@ -161864,14 +177196,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Sequence trimming", "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", - "Nucleic acid sequence analysis", + "Sequence trimming", "Validation" ], "edam_topic": [], @@ -161885,11 +177217,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_starsolo", "htseq_count", "multiqc", - "fastqc", + "rna_starsolo", "__FLATTEN__", + "fastqc", "cutadapt" ], "update_time": "2023-05-08", @@ -161900,18 +177232,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "af3f40cba4d7afa6", @@ -161924,14 +177256,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-05", "versions": 7 @@ -161960,18 +177292,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "e826584d78b69467", @@ -161984,14 +177316,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-05", "versions": 0 @@ -162020,18 +177352,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "cef68481b305a516", @@ -162044,14 +177376,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-05", "versions": 2 @@ -162061,18 +177393,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "d126940d33e63036", @@ -162085,15 +177417,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_cat", "deg_annotate", "fastqc", - "deseq2", - "cutadapt", - "tp_cat" + "hisat2", + "deseq2" ], "update_time": "2023-05-05", "versions": 0 @@ -162103,15 +177435,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "05950987aa2eba5b", @@ -162124,13 +177456,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "featurecounts", + "Filter1", "sort1", + "featurecounts", + "trimmomatic", "multiqc", - "hisat2", "fastqc", - "Filter1", + "hisat2", "deseq2" ], "update_time": "2023-05-05", @@ -162141,18 +177473,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "16f4846b4d6bc155", @@ -162165,14 +177497,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "rna_star", - "featurecounts", "Filter1", + "featurecounts", "multiqc", + "tp_sort_header_tool", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "deseq2" ], "update_time": "2023-05-05", "versions": 0 @@ -162182,18 +177514,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "07c97b9e59c0218f", @@ -162206,14 +177538,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 13 @@ -162223,18 +177555,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "9b1afa59c087eacd", @@ -162247,14 +177579,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162264,18 +177596,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "981d7b02416b7734", @@ -162288,14 +177620,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_sort_header_tool", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162305,18 +177637,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "ae5dca8108d1a8a6", @@ -162329,13 +177661,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 5 @@ -162345,18 +177677,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "56599572e0364e2a", @@ -162369,13 +177701,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 1 @@ -162385,15 +177717,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "e4ddf33ee5b5e259", @@ -162407,18 +177739,18 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", + "Filter1", + "featurecounts", "trimmomatic", - "join1", "Cut1", - "featurecounts", "tp_replace_in_line", - "CONVERTER_uncompressed_to_gz", - "hisat2", "multiqc", + "CONVERTER_uncompressed_to_gz", "deg_annotate", + "join1", "fastqc", - "Filter1", + "hisat2", + "ggplot2_heatmap2", "deseq2" ], "update_time": "2023-05-04", @@ -162429,13 +177761,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "158b5d9107a05d95", @@ -162448,9 +177780,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2023-05-04", "versions": 1 @@ -162460,18 +177792,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "0c567180448d8774", @@ -162484,15 +177816,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "featurecounts", "Filter1", + "featurecounts", + "trimmomatic", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", - "fastqc", - "deseq2", - "cutadapt" + "fastqc", + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162502,18 +177834,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "2cef9a1633e0a067", @@ -162527,20 +177859,20 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", + "Filter1", "Add_a_column1", - "rna_star", - "Cut1", - "join1", "featurecounts", - "length_and_gc_content", - "Filter1", + "Cut1", "multiqc", "ChangeCase", "deg_annotate", + "join1", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "length_and_gc_content", + "cutadapt", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162550,18 +177882,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "897e9d7432d231e9", @@ -162574,14 +177906,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "volcanoplot", - "rna_star", - "featurecounts", "Filter1", + "featurecounts", "multiqc", + "volcanoplot", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "deseq2" ], "update_time": "2023-05-04", "versions": 5 @@ -162591,18 +177923,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "6b34c95a247d15e3", @@ -162615,14 +177947,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", "sort1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162632,20 +177964,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Read summarisation", - "Statistical calculation", - "Primer removal", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Sequence trimming", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "85aede91db0122e4", @@ -162658,30 +177990,30 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rseqc_read_distribution", - "samtools_view", + "rseqc_geneBody_coverage", + "samtool_filter2", + "join1", "fastqc", - "samtools_idxstats", - "tp_replace_in_line", + "rna_star", + "__TAG_FROM_FILE__", + "collection_element_identifiers", "sort1", - "deseq2", - "join1", + "Filter1", + "samtools_idxstats", "featurecounts", - "gtftobed12", - "cat1", - "ggplot2_heatmap2", + "multiqc", + "deg_annotate", + "cutadapt", + "samtools_view", + "deseq2", "picard_MarkDuplicates", - "rna_star", - "collection_element_identifiers", - "Cut1", - "__TAG_FROM_FILE__", + "cat1", "filter_tabular", - "samtool_filter2", - "rseqc_geneBody_coverage", - "deg_annotate", - "multiqc", - "Filter1", - "cutadapt" + "tp_replace_in_line", + "rseqc_read_distribution", + "gtftobed12", + "Cut1", + "ggplot2_heatmap2" ], "update_time": "2023-05-04", "versions": 0 @@ -162691,18 +178023,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "3ce9dc804780e4a1", @@ -162716,11 +178048,11 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 1 @@ -162730,18 +178062,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "677ef3322366c953", @@ -162754,14 +178086,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "featurecounts", "Filter1", + "featurecounts", + "trimmomatic", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162771,18 +178103,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "de1c04a2caf70647", @@ -162795,14 +178127,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 1 @@ -162812,18 +178144,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "83680c1c6dffb05b", @@ -162836,14 +178168,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 0 @@ -162853,18 +178185,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "000cdc969e9f0886", @@ -162877,14 +178209,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 8 @@ -162894,18 +178226,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "421adea2f259ec26", @@ -162918,13 +178250,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-04", "versions": 1 @@ -162934,18 +178266,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "8cab31db0bd3ff52", @@ -162958,15 +178290,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_cat", "deg_annotate", "fastqc", - "deseq2", - "cutadapt", - "tp_cat" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 1 @@ -162976,18 +178308,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "9898348d95033af2", @@ -163000,13 +178332,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 3 @@ -163016,18 +178348,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "39d56981a6854d82", @@ -163040,14 +178372,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 4 @@ -163057,18 +178389,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "1ad81f95ace878ea", @@ -163081,13 +178413,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_star", - "featurecounts", "Filter1", + "featurecounts", "multiqc", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "deseq2" ], "update_time": "2023-05-03", "versions": 0 @@ -163097,18 +178429,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "879d4fb110a61f7a", @@ -163121,13 +178453,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 0 @@ -163137,18 +178469,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "aed93da6fd6e4e13", @@ -163161,13 +178493,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 0 @@ -163177,17 +178509,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "10acf4f497172400", @@ -163200,14 +178532,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", - "hisat2", - "tabular_to_csv", + "featurecounts", + "cutadapt", "deg_annotate", + "tabular_to_csv", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 1 @@ -163217,18 +178549,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "d7a65f577fe5f16b", @@ -163241,14 +178573,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", "sort1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 0 @@ -163258,21 +178590,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "Gene functional annotation", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Read summarisation", - "Statistical calculation", - "Primer removal", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Sequence trimming", - "Gene functional annotation", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "e1fd89e7248b6661", @@ -163285,34 +178617,34 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "rseqc_geneBody_coverage", + "samtool_filter2", "table_compute", - "rseqc_read_distribution", - "samtools_view", - "ChangeCase", + "join1", "fastqc", - "samtools_idxstats", - "tp_replace_in_line", + "rna_star", + "__TAG_FROM_FILE__", + "collection_element_identifiers", "sort1", - "deseq2", + "Filter1", "Add_a_column1", - "join1", + "samtools_idxstats", "featurecounts", - "gtftobed12", - "goseq", - "cat1", - "ggplot2_heatmap2", + "multiqc", + "deg_annotate", + "cutadapt", + "samtools_view", + "deseq2", "picard_MarkDuplicates", - "rna_star", - "collection_element_identifiers", - "Cut1", - "__TAG_FROM_FILE__", + "cat1", "filter_tabular", - "samtool_filter2", - "rseqc_geneBody_coverage", - "deg_annotate", - "multiqc", - "Filter1", - "cutadapt" + "tp_replace_in_line", + "rseqc_read_distribution", + "gtftobed12", + "ChangeCase", + "Cut1", + "ggplot2_heatmap2", + "goseq" ], "update_time": "2023-05-03", "versions": 0 @@ -163322,18 +178654,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "897dfa78c3b25356", @@ -163346,14 +178678,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-03", "versions": 1 @@ -163363,18 +178695,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "aa94c77b720a2810", @@ -163388,11 +178720,11 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 0 @@ -163402,18 +178734,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "7ef245f5ae3b916d", @@ -163427,17 +178759,17 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", - "join1", - "Cut1", - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", + "Cut1", "multiqc", - "hisat2", "deg_annotate", + "join1", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2023-05-02", "versions": 2 @@ -163447,18 +178779,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "544cb12a16f283b8", @@ -163471,14 +178803,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 1 @@ -163488,17 +178820,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Differential gene expression analysis", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "8fb691706f47527a", @@ -163512,16 +178844,16 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", - "rna_star", - "join1", - "Cut1", - "featurecounts", "Filter1", + "featurecounts", + "Cut1", "deg_annotate", + "join1", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2023-05-02", "versions": 4 @@ -163531,18 +178863,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "c3bb21f20a3ce689", @@ -163555,15 +178887,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "tp_cat", "deg_annotate", "fastqc", - "deseq2", - "cutadapt", - "tp_cat" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 0 @@ -163573,18 +178905,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "3bc45aaed5da1058", @@ -163597,14 +178929,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "cutadapt", "multiqc", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 7 @@ -163614,14 +178946,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Sequencing quality control", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence alignment", - "Validation" + "Sequence trimming", + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "eaa841e6b7384633", @@ -163635,10 +178967,10 @@ "tags": [], "tools": [ "trimmomatic", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2023-05-02", "versions": 0 @@ -163648,10 +178980,10 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Differential gene expression analysis", + "RNA-Seq quantification", "Read summarisation", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "42305ed876d19d08", @@ -163665,13 +178997,13 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", - "join1", - "Cut1", - "featurecounts", "Filter1", "sort1", + "featurecounts", "deg_annotate", + "join1", + "Cut1", + "ggplot2_heatmap2", "deseq2" ], "update_time": "2023-05-02", @@ -163682,18 +179014,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "8c40b4a911517cc5", @@ -163706,13 +179038,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 0 @@ -163722,16 +179054,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Validation", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Validation" ], "edam_topic": [], "id": "1ab66d382630afa7", @@ -163745,10 +179077,10 @@ "tags": [], "tools": [ "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "cutadapt" + "hisat2" ], "update_time": "2023-05-02", "versions": 0 @@ -163758,21 +179090,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "Gene functional annotation", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Read summarisation", - "Statistical calculation", - "Primer removal", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Sequence trimming", - "Gene functional annotation", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "75113a1b41904d2a", @@ -163785,34 +179117,34 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "rseqc_geneBody_coverage", + "samtool_filter2", "table_compute", - "rseqc_read_distribution", - "samtools_view", - "ChangeCase", + "join1", "fastqc", - "samtools_idxstats", - "tp_replace_in_line", + "rna_star", + "__TAG_FROM_FILE__", + "collection_element_identifiers", "sort1", - "deseq2", + "Filter1", "Add_a_column1", - "join1", + "samtools_idxstats", "featurecounts", - "gtftobed12", - "goseq", - "cat1", - "ggplot2_heatmap2", + "multiqc", + "deg_annotate", + "cutadapt", + "samtools_view", + "deseq2", "picard_MarkDuplicates", - "rna_star", - "collection_element_identifiers", - "Cut1", - "__TAG_FROM_FILE__", + "cat1", "filter_tabular", - "samtool_filter2", - "rseqc_geneBody_coverage", - "deg_annotate", - "multiqc", - "Filter1", - "cutadapt" + "tp_replace_in_line", + "rseqc_read_distribution", + "gtftobed12", + "ChangeCase", + "Cut1", + "ggplot2_heatmap2", + "goseq" ], "update_time": "2023-05-02", "versions": 0 @@ -163822,18 +179154,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "dce29c35dfac48b1", @@ -163846,14 +179178,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 0 @@ -163888,18 +179220,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", - "Read summarisation", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "RNA-Seq analysis", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "7ad277dd448e57b3", @@ -163912,13 +179244,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_star", - "trim_galore", - "featurecounts", "Filter1", "sort1", + "featurecounts", "multiqc", + "trim_galore", "fastqc", + "rna_star", "deseq2" ], "update_time": "2023-05-02", @@ -163929,9 +179261,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "5a0fc3b91ae47788", @@ -163944,8 +179276,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2023-05-02", "versions": 0 @@ -163955,18 +179287,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "978953f492b2b914", @@ -163979,13 +179311,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2023-05-02", "versions": 0 @@ -163995,15 +179327,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "14184bc2580a131f", @@ -164016,12 +179348,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", "featurecounts", - "hisat2", + "trimmomatic", "multiqc", "deg_annotate", "fastqc", + "hisat2", "deseq2" ], "update_time": "2023-04-29", @@ -164032,15 +179364,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "f19d63d7c9a48160", @@ -164053,13 +179385,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "trimmomatic", "multiqc", "deg_annotate", "fastqc", + "hisat2", "deseq2" ], "update_time": "2023-04-26", @@ -164070,17 +179402,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Sequence alignment", + "Sequence contamination filtering", + "Statistical calculation", "Read binning", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Sequence contamination filtering", - "RNA-Seq analysis", - "Statistical calculation" + "Read mapping", + "RNA-Seq analysis" ], "edam_topic": [], "id": "25f65a29ce3c3ee0", @@ -164094,9 +179426,9 @@ "tags": [], "tools": [ "trimmomatic", + "fastqc", "trim_galore", "bbtools_bbduk", - "fastqc", "cutadapt" ], "update_time": "2023-04-09", @@ -164107,19 +179439,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene prediction", + "Genome annotation", + "Genome assembly", + "Sequence assembly", + "Mapping assembly", + "Multilocus sequence typing", "Base-calling", + "Cross-assembly", + "Coding region prediction", "De-novo assembly", - "Sequence assembly", - "Genome assembly", "Variant calling", - "Multilocus sequence typing", - "Gene prediction", "Antimicrobial resistance prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction", - "Mapping assembly", - "Cross-assembly" + "Taxonomic classification" ], "edam_topic": [], "id": "59618ed15510f531", @@ -164139,13 +179471,13 @@ "annotation" ], "tools": [ - "abricate", + "prokka", "flye", - "porechop", "kraken2", - "mlst", + "abricate", + "porechop", "medaka_consensus_pipeline", - "prokka" + "mlst" ], "update_time": "2023-03-22", "versions": 2 @@ -164155,21 +179487,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Base-calling", - "De-novo assembly", + "Gene prediction", + "Genome annotation", + "Genome assembly", "Sequence assembly", + "Mapping assembly", + "Multilocus sequence typing", "Sequencing quality control", - "Genome assembly", + "Base-calling", + "Cross-assembly", + "Coding region prediction", + "De-novo assembly", "Variant calling", - "Multilocus sequence typing", - "Gene prediction", + "Filtering", "Antimicrobial resistance prediction", - "Genome annotation", - "Taxonomic classification", - "Coding region prediction", - "Mapping assembly", - "Cross-assembly" + "Taxonomic classification" ], "edam_topic": [], "id": "c997a34b55425155", @@ -164189,14 +179521,14 @@ "annotation" ], "tools": [ - "abricate", + "prokka", "flye", - "porechop", "kraken2", - "filtlong", - "mlst", + "abricate", + "porechop", "medaka_consensus_pipeline", - "prokka" + "filtlong", + "mlst" ], "update_time": "2023-03-16", "versions": 4 @@ -164207,11 +179539,11 @@ "doi": "", "edam_operation": [ "Gene prediction", - "Antimicrobial resistance prediction", - "Genome annotation", - "Taxonomic classification", "Coding region prediction", - "Multilocus sequence typing" + "Genome annotation", + "Multilocus sequence typing", + "Antimicrobial resistance prediction", + "Taxonomic classification" ], "edam_topic": [], "id": "e20172eb0f30d6cd", @@ -164230,10 +179562,10 @@ "annotation" ], "tools": [ - "mlst", + "prokka", "abricate", - "kraken2", - "prokka" + "mlst", + "kraken2" ], "update_time": "2023-03-16", "versions": 1 @@ -164245,17 +179577,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "a8ec08a1408cd6e7", @@ -164270,15 +179602,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2023-02-23", "versions": 1 @@ -164288,9 +179620,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "bc2994ad0fbe07cd", @@ -164315,15 +179647,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7d268e7209a68e2e", @@ -164338,13 +179670,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -164356,19 +179688,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "32d28f800adcea42", @@ -164383,23 +179715,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -164411,19 +179743,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "52056336f24eccf6", @@ -164438,23 +179770,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2023-01-19", "versions": 1 @@ -164466,15 +179798,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "b191da6e594747fb", @@ -164489,13 +179821,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2023-01-19", "versions": 1 @@ -164507,15 +179839,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "e92b4d8dfa2f1cf7", @@ -164530,13 +179862,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -164548,19 +179880,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "3e7fcfd23872ad0d", @@ -164575,23 +179907,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -164603,15 +179935,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "7ad9410e36ee9ea1", @@ -164626,13 +179958,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-12-01", "versions": 1 @@ -164644,17 +179976,17 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "57b558e1a76c09e1", @@ -164669,15 +180001,15 @@ "cutnrun" ], "tools": [ - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "tp_grep_tool", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "bedtools_bamtobed", + "cutadapt", + "picard_MarkDuplicates" ], "update_time": "2022-12-01", "versions": 1 @@ -164687,9 +180019,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", "Coding region prediction", + "Genome visualisation", "Genome annotation" ], "edam_topic": [], @@ -164703,8 +180035,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2022-11-10", "versions": 1 @@ -164717,12 +180049,12 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", + "Genome assembly", + "Sequence alignment", "Data handling", + "Sequence assembly validation", "Scaffolding", - "Genome assembly", "Mapping", - "Sequence alignment", "Transcriptome assembly" ], "edam_topic": [], @@ -164741,19 +180073,19 @@ "yahs" ], "tools": [ - "bellerophon", - "bedtools_bamtobed", - "__EXTRACT_DATASET__", - "pretext_map", - "gfa_to_fa", + "bwa_mem2", "param_value_from_file", + "sort1", + "__EXTRACT_DATASET__", "samtools_sort", "yahs", - "sort1", - "busco", - "bwa_mem2", + "gfastats", + "gfa_to_fa", "pretext_snapshot", - "gfastats" + "bedtools_bamtobed", + "busco", + "pretext_map", + "bellerophon" ], "update_time": "2022-11-10", "versions": 5 @@ -164766,14 +180098,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", "Sequence alignment", - "Sequence assembly validation", "Scaffolding", - "Genome assembly", - "Mapping", - "Transcriptome assembly" + "Transcriptome assembly", + "De-novo assembly", + "Data handling", + "Sequence assembly validation", + "Mapping" ], "edam_topic": [], "id": "e07866576cc2f467", @@ -164791,20 +180123,20 @@ "salsa" ], "tools": [ - "bellerophon", - "bedtools_bamtobed", + "bwa_mem2", + "param_value_from_file", + "sort1", "__EXTRACT_DATASET__", - "pretext_map", "tp_find_and_replace", + "samtools_sort", + "gfastats", "gfa_to_fa", - "param_value_from_file", + "pretext_snapshot", "salsa", - "samtools_sort", - "sort1", + "bedtools_bamtobed", "busco", - "bwa_mem2", - "pretext_snapshot", - "gfastats" + "pretext_map", + "bellerophon" ], "update_time": "2022-11-10", "versions": 5 @@ -164817,16 +180149,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "7909da83448d8bf4", @@ -164845,16 +180177,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2022-11-10", "versions": 2 @@ -164868,17 +180200,17 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "98d3def7da131b4c", @@ -164896,19 +180228,19 @@ "hifiasm" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "gfa_to_fa", "param_value_from_file", + "Cut1", "tp_grep_tool", "tp_replace_in_line", + "gfa_to_fa", + "gfastats", "merqury", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2022-11-10", "versions": 2 @@ -164938,9 +180270,9 @@ "bionano" ], "tools": [ - "gfastats", "param_value_from_file", - "bionano_scaffold" + "bionano_scaffold", + "gfastats" ], "update_time": "2022-11-10", "versions": 2 @@ -164953,14 +180285,14 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", - "Phasing", - "k-mer counting", "Read binning", + "Genome assembly", + "Phasing", "Scaffolding", - "Genome assembly" + "k-mer counting", + "De-novo assembly", + "Pairwise sequence alignment", + "Data handling" ], "edam_topic": [], "id": "094655df3ccd0b00", @@ -164978,13 +180310,13 @@ "purge_dups" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", "param_value_from_file", - "minimap2", "merqury", + "gfastats", + "tp_easyjoin_tool", + "minimap2", "purge_dups", - "gfastats" + "tp_awk_tool" ], "update_time": "2022-11-10", "versions": 1 @@ -164997,16 +180329,16 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", - "Pairwise sequence alignment", + "Read binning", + "Genome assembly", "Phasing", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", - "Read binning", + "De-novo assembly", + "Pairwise sequence alignment", "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" + "Data handling" ], "edam_topic": [], "id": "1dcc1b25c9091fbf", @@ -165025,16 +180357,16 @@ ], "tools": [ "cat1", - "tp_easyjoin_tool", - "Add_a_column1", - "gfastats", - "Cut1", - "tp_awk_tool", "param_value_from_file", - "minimap2", + "Add_a_column1", "merqury", + "gfastats", "busco", - "purge_dups" + "tp_easyjoin_tool", + "minimap2", + "Cut1", + "purge_dups", + "tp_awk_tool" ], "update_time": "2022-11-10", "versions": 1 @@ -165047,17 +180379,17 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "De-novo assembly", + "Genome assembly", "Phasing", - "k-mer counting", - "Sequence assembly validation", "Scaffolding", "Primer removal", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", "Read pre-processing", - "Genome assembly", "Sequence trimming", - "Transcriptome assembly" + "Sequence assembly validation", + "Data handling" ], "edam_topic": [], "id": "afab89bc468da8b3", @@ -165075,19 +180407,19 @@ "hifiasm" ], "tools": [ - "tp_easyjoin_tool", - "tp_awk_tool", - "Cut1", - "gfa_to_fa", "param_value_from_file", + "Cut1", "tp_grep_tool", "tp_replace_in_line", + "gfa_to_fa", + "gfastats", "merqury", "Convert characters1", "busco", + "tp_easyjoin_tool", "cutadapt", "hifiasm", - "gfastats" + "tp_awk_tool" ], "update_time": "2022-11-10", "versions": 2 @@ -165117,8 +180449,8 @@ "genome_profiling" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2022-11-10", "versions": 2 @@ -165130,15 +180462,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Enrichment analysis", "Peak calling", - "Sequencing quality control", - "Gene regulatory network analysis", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Gene regulatory network analysis", "Sequence trimming", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis" ], "edam_topic": [], "id": "9787c8b7adeedb0c", @@ -165153,13 +180485,13 @@ "chip" ], "tools": [ - "tp_grep_tool", - "samtool_filter2", + "bowtie2", + "macs2_callpeak", "wig_to_bigWig", + "samtool_filter2", + "cutadapt", "multiqc", - "macs2_callpeak", - "bowtie2", - "cutadapt" + "tp_grep_tool" ], "update_time": "2022-10-27", "versions": 1 @@ -165171,19 +180503,19 @@ ], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Read mapping", - "Enrichment analysis", "Peak calling", + "Primer removal", "Sequencing quality control", "Formatting", - "Gene regulatory network analysis", - "Primer removal", "Read pre-processing", + "Gene regulatory network analysis", + "Sequence alignment analysis", + "Data handling", "Sequence trimming", - "Mapping", - "Validation" + "Validation", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "6b3df543536faf8c", @@ -165198,23 +180530,23 @@ "atacseq" ], "tools": [ - "cat1", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "bedtools_slopbed", - "tp_awk_tool", - "bedtools_mergebed", - "samtools_view", - "tp_grep_tool", + "macs2_callpeak", "wig_to_bigWig", - "multiqc", + "bedtools_coveragebed", + "pe_histogram", "samtools_idxstats", - "macs2_callpeak", + "cat1", + "tp_grep_tool", + "bedtools_mergebed", + "multiqc", + "bedtools_bamtobed", + "bedtools_slopbed", "bamFilter", - "bedtools_coveragebed", "cutadapt", - "pe_histogram" + "samtools_view", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2022-10-27", "versions": 1 @@ -165242,17 +180574,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", - "snpSift_filter" + "gops_merge_1", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-10-27", "versions": 1 @@ -165278,20 +180610,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-10-27", "versions": 1 @@ -165303,14 +180635,14 @@ ], "doi": "", "edam_operation": [ - "De-novo assembly", - "Phasing", - "k-mer counting", - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", - "Transcriptome assembly" + "Phasing", + "Scaffolding", + "Transcriptome assembly", + "k-mer counting", + "De-novo assembly", + "Sequence assembly validation" ], "edam_topic": [], "id": "df11f09771e73e04", @@ -165331,11 +180663,11 @@ "busco" ], "tools": [ - "meryl", - "quast", "fasta-stats", + "merqury", + "meryl", "busco", - "merqury" + "quast" ], "update_time": "2022-10-17", "versions": 7 @@ -165345,12 +180677,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Sequencing quality control" ], "edam_topic": [], "id": "954318db8c8d9219", @@ -165368,10 +180700,10 @@ "counts" ], "tools": [ - "fastqc", - "multiqc", "salmon", - "trimmomatic" + "trimmomatic", + "multiqc", + "fastqc" ], "update_time": "2022-10-11", "versions": 19 @@ -165382,10 +180714,10 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "RNA-Seq analysis", - "Differential gene expression analysis", "Gene expression analysis", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq quantification", + "RNA-Seq analysis" ], "edam_topic": [], "id": "13a2c5bd07705985", @@ -165398,10 +180730,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "salmon", "tab2fasta", - "deseq2", - "Filter1" + "Filter1", + "salmon", + "deseq2" ], "update_time": "2022-09-29", "versions": 14 @@ -165431,12 +180763,12 @@ "genome_assembly" ], "tools": [ - "hifiadapterfilt", + "bandage_info", + "fasta-stats", "gfa_to_fa", "bandage_image", - "fasta-stats", - "hifiasm", - "bandage_info" + "hifiadapterfilt", + "hifiasm" ], "update_time": "2022-09-19", "versions": 32 @@ -165459,13 +180791,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "ggplot2_point", - "tp_cut_tool", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "tp_cut_tool", + "ggplot2_point", + "datamash_ops" ], "update_time": "2022-08-18", "versions": 2 @@ -165475,24 +180807,24 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Pairwise sequence alignment", - "Phasing", "Visualisation", - "Scaffolding", - "Read pre-processing", - "Sequence trimming", - "Genome assembly", - "Genome indexing", - "Generation", - "Read mapping", - "Sequence alignment", "Read binning", + "Sequence alignment", + "Primer removal", + "Scaffolding", + "Transcriptome assembly", "k-mer counting", + "Sequence trimming", "Sequence assembly validation", - "Primer removal", + "Read mapping", "Mapping", - "Transcriptome assembly" + "Genome assembly", + "Phasing", + "Pairwise sequence alignment", + "De-novo assembly", + "Generation", + "Genome indexing", + "Read pre-processing" ], "edam_topic": [], "id": "434127690544d0e9", @@ -165507,32 +180839,32 @@ "assembly" ], "tools": [ + "collapse_dataset", + "tp_find_and_replace", "bedtools_bamtobed", "tp_grep_tool", - "salsa", - "minimap2", - "meryl", - "bionano_scaffold", - "tp_cut_tool", - "pretext_map", - "tp_find_and_replace", + "param_value_from_file", "sort1", - "pretext_snapshot", - "purge_dups", "Add_a_column1", - "bellerophon", - "collapse_dataset", - "gfa_to_fa", - "param_value_from_file", - "quast", + "pretext_snapshot", "Convert characters1", + "salsa", "busco", - "hifiasm", - "cat1", + "quast", "bwa_mem", "genomescope", "cutadapt", - "merqury" + "hifiasm", + "purge_dups", + "cat1", + "merqury", + "meryl", + "gfa_to_fa", + "bionano_scaffold", + "pretext_map", + "minimap2", + "bellerophon", + "tp_cut_tool" ], "update_time": "2022-08-04", "versions": 1 @@ -165542,12 +180874,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", + "Sequence contamination filtering", "Sequence composition calculation", + "Statistical calculation", "Genome assembly", - "Sequence contamination filtering", - "Sequencing quality control", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Sequencing quality control" ], "edam_topic": [], "id": "813a4938397cf6ee", @@ -165563,10 +180895,10 @@ "bacterial" ], "tools": [ - "fastqc", + "bandage_image", "spades", "fastp", - "bandage_image" + "fastqc" ], "update_time": "2022-07-18", "versions": 3 @@ -165576,8 +180908,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Sequencing quality control" + "Sequencing quality control", + "Mapping" ], "edam_topic": [], "id": "5cf5334877cc1297", @@ -165592,17 +180924,17 @@ "ga-virreport-confidence" ], "tools": [ - "ncbi_blastdbcmd_wrapper", - "bedtools_genomecoveragebed", - "qualimap_bamqc", - "tp_awk_tool", - "bedtools_maskfastabed", + "bowtie_wrapper", "bcftools_consensus", "bcftools_call", - "sam_to_bam", "ncbi_blastn_wrapper", + "sam_to_bam", + "bedtools_maskfastabed", "bcftools_mpileup", - "bowtie_wrapper" + "bedtools_genomecoveragebed", + "ncbi_blastdbcmd_wrapper", + "tp_awk_tool", + "qualimap_bamqc" ], "update_time": "2022-06-28", "versions": 1 @@ -165614,20 +180946,20 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "De-novo assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Local alignment", - "Sequence trimming", "Sequence contamination filtering", "Statistical calculation", - "Global alignment", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Local alignment", + "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Read pre-processing", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Sequence trimming", + "Global alignment" ], "edam_topic": [], "id": "dccc8fb49d61ac33", @@ -165642,18 +180974,18 @@ "ga-virreport" ], "tools": [ - "velveth", - "EMBOSS: getorf42", + "bowtie_wrapper", + "ncbi_makeblastdb", "ncbi_tblastn_wrapper", + "ncbi_blastn_wrapper", + "fastp", "umi_tools_extract", "velvetg", - "fastp", - "ncbi_makeblastdb", - "cap3", + "velveth", "fastqc", - "ncbi_blastn_wrapper", - "bowtie_wrapper", - "cutadapt" + "cap3", + "cutadapt", + "EMBOSS: getorf42" ], "update_time": "2022-06-28", "versions": 1 @@ -165665,20 +180997,20 @@ ], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "De-novo assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Local alignment", - "Sequence trimming", "Sequence contamination filtering", "Statistical calculation", - "Global alignment", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Local alignment", + "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Read pre-processing", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Sequence trimming", + "Global alignment" ], "edam_topic": [], "id": "94c7fdcbbc7b428a", @@ -165693,19 +181025,19 @@ "ga-virreport" ], "tools": [ - "velveth", - "EMBOSS: getorf42", + "bowtie_wrapper", + "ncbi_makeblastdb", "ncbi_tblastn_wrapper", + "ncbi_blastn_wrapper", "cat_multiple", + "fastp", "umi_tools_extract", "velvetg", - "fastp", - "ncbi_makeblastdb", - "cap3", + "velveth", "fastqc", - "ncbi_blastn_wrapper", - "bowtie_wrapper", - "cutadapt" + "cap3", + "cutadapt", + "EMBOSS: getorf42" ], "update_time": "2022-06-28", "versions": 2 @@ -165733,18 +181065,18 @@ "generic" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-06-06", "versions": 1 @@ -165770,18 +181102,18 @@ "generic" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "datamash_ops" ], "update_time": "2022-06-06", "versions": 1 @@ -165793,14 +181125,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "06ba34da322f46f1", @@ -165816,18 +181148,18 @@ "generic" ], "tools": [ + "samtools_stats", + "snpEff", + "lofreq_viterbi", "lofreq_filter", + "fastp", + "multiqc", + "lofreq_indelqual", "bwa_mem", - "picard_MarkDuplicates", - "samtools_view", "snpEff_build_gb", - "snpEff", - "samtools_stats", - "fastp", - "lofreq_viterbi", "lofreq_call", - "lofreq_indelqual", - "multiqc" + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-06-06", "versions": 1 @@ -165837,13 +181169,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence assembly validation", - "Visualisation", "Gene prediction", + "Coding region prediction", "Genome annotation", + "Visualisation", "Genome assembly", - "Coding region prediction" + "Sequence assembly validation", + "Aggregation" ], "edam_topic": [], "id": "8f7d5ebead46a6d0", @@ -165856,10 +181188,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "quast", "prokka", + "trimmomatic", "spades", + "quast", "unicycler" ], "update_time": "2022-06-04", @@ -165881,12 +181213,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "stacks2_cstacks", - "stacks2_gstacks", - "stacks2_populations", "stacks2_tsv2bam", + "stacks2_ustacks", + "stacks2_populations", + "stacks2_cstacks", "stacks2_sstacks", - "stacks2_ustacks" + "stacks2_gstacks" ], "update_time": "2022-05-31", "versions": 8 @@ -165896,9 +181228,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Sequence alignment" ], "edam_topic": [], "id": "f7adc76331620f34", @@ -165911,12 +181243,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "stacks2_gstacks", - "samtools_view", - "stacks2_populations", - "samtools_stats", "bwa_mem2", - "multiqc" + "samtools_stats", + "multiqc", + "stacks2_populations", + "stacks2_gstacks", + "samtools_view" ], "update_time": "2022-05-31", "versions": 23 @@ -165926,9 +181258,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Validation", "Sequencing quality control", - "Sequence alignment", - "Validation" + "Sequence alignment" ], "edam_topic": [], "id": "44bad90b676d58f6", @@ -165941,10 +181273,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "multiqc", + "bwa_mem2", "samtools_stats", - "samtools_view", - "bwa_mem2" + "multiqc", + "samtools_view" ], "update_time": "2022-05-19", "versions": 7 @@ -165965,8 +181297,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "stacks2_populations", - "stacks2_gstacks" + "stacks2_gstacks", + "stacks2_populations" ], "update_time": "2022-05-18", "versions": 2 @@ -165987,11 +181319,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "stacks2_cstacks", - "stacks2_gstacks", - "stacks2_populations", "stacks2_tsv2bam", - "stacks2_sstacks" + "stacks2_populations", + "stacks2_cstacks", + "stacks2_sstacks", + "stacks2_gstacks" ], "update_time": "2022-05-18", "versions": 2 @@ -166022,13 +181354,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", "Sequence contamination filtering", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Sequencing quality control", "Validation" ], "edam_topic": [], @@ -166042,10 +181374,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", "fastp", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2022-05-18", "versions": 29 @@ -166055,18 +181387,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "67191ea9fe977e08", @@ -166079,14 +181411,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "Filter1", "featurecounts", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "Filter1", - "deseq2", - "cutadapt" + "hisat2", + "cutadapt", + "deseq2" ], "update_time": "2022-05-18", "versions": 1 @@ -166096,18 +181428,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "b452e983e08b9298", @@ -166120,13 +181452,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-14", "versions": 0 @@ -166136,18 +181468,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "f5c0b0bc5e023e42", @@ -166160,14 +181492,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-12", "versions": 4 @@ -166177,18 +181509,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "975ddb0eb436f1fd", @@ -166201,14 +181533,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-12", "versions": 5 @@ -166218,20 +181550,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", + "Statistical calculation", + "Sequence alignment", "Differential gene expression analysis", + "Primer removal", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Read summarisation", - "Statistical calculation", - "Primer removal", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", - "Sequence trimming", "Validation", - "RNA-Seq quantification" + "Sequence trimming", + "RNA-Seq quantification", + "Read summarisation", + "Data handling", + "RNA-Seq analysis" ], "edam_topic": [], "id": "ce7f6a1c824920e2", @@ -166244,25 +181576,25 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rseqc_read_distribution", - "samtools_view", - "rseqc_infer_experiment", + "rseqc_geneBody_coverage", "fastqc", - "samtools_idxstats", - "tp_replace_in_line", - "deseq2", - "featurecounts", - "gtftobed12", - "cat1", - "picard_MarkDuplicates", "rna_star", - "collection_element_identifiers", "__TAG_FROM_FILE__", - "rseqc_geneBody_coverage", - "deg_annotate", - "multiqc", + "rseqc_infer_experiment", + "collection_element_identifiers", "Filter1", - "cutadapt" + "samtools_idxstats", + "featurecounts", + "multiqc", + "deg_annotate", + "cutadapt", + "samtools_view", + "deseq2", + "picard_MarkDuplicates", + "cat1", + "tp_replace_in_line", + "rseqc_read_distribution", + "gtftobed12" ], "update_time": "2022-05-12", "versions": 0 @@ -166272,18 +181604,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5ce00d3eab862f4e", @@ -166296,13 +181628,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-12", "versions": 0 @@ -166312,18 +181644,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "fb644a9649f36f40", @@ -166336,15 +181668,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", - "gff_filter_by_attribute", "Filter1", "sort1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", + "gff_filter_by_attribute", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-12", "versions": 2 @@ -166354,15 +181686,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", + "Statistical calculation", "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", + "Sequence composition calculation", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a1c59e9f5c7327d2", @@ -166375,13 +181707,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trimmomatic", - "featurecounts", "Filter1", - "hisat2", + "featurecounts", + "trimmomatic", "multiqc", "deg_annotate", "fastqc", + "hisat2", "deseq2" ], "update_time": "2022-05-12", @@ -166392,18 +181724,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "301fdb29c513ffbe", @@ -166416,14 +181748,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-12", "versions": 0 @@ -166433,18 +181765,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "afd9a8bbc07f9c3f", @@ -166457,14 +181789,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-11", "versions": 0 @@ -166474,18 +181806,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "374311292d72c9f9", @@ -166498,14 +181830,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-11", "versions": 0 @@ -166515,18 +181847,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", "Read pre-processing", - "RNA-Seq analysis", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "3c727d5cd349a846", @@ -166539,14 +181871,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "featurecounts", "Filter1", + "featurecounts", + "cutadapt", "multiqc", - "hisat2", "deg_annotate", "fastqc", - "deseq2", - "cutadapt" + "hisat2", + "deseq2" ], "update_time": "2022-05-11", "versions": 0 @@ -166556,9 +181888,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "acaca80c4a0c76c8", @@ -166571,8 +181903,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2022-05-11", "versions": 2 @@ -166582,18 +181914,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", - "RNA-Seq analysis", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "ae773dfaa074cb72", @@ -166607,17 +181939,17 @@ "tags": [], "tools": [ "cat1", - "ggplot2_heatmap2", - "rna_star", - "join1", - "Cut1", - "featurecounts", "Filter1", + "featurecounts", + "Cut1", "multiqc", "deg_annotate", + "join1", "fastqc", - "deseq2", - "cutadapt" + "rna_star", + "cutadapt", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2022-05-03", "versions": 3 @@ -166629,10 +181961,10 @@ ], "doi": "", "edam_operation": [ - "Scaffolding", - "Genome assembly", "Pairwise sequence alignment", - "Read binning" + "Scaffolding", + "Read binning", + "Genome assembly" ], "edam_topic": [], "id": "e5dfeff4a3068f36", @@ -166649,8 +181981,8 @@ "hifi" ], "tools": [ - "minimap2", "fasta-stats", + "minimap2", "purge_dups" ], "update_time": "2022-03-25", @@ -166663,10 +181995,10 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Formatting", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Formatting", + "Sequencing quality control" ], "edam_topic": [], "id": "db322fe56af3ee5b", @@ -166684,8 +182016,8 @@ "qc" ], "tools": [ - "picard_SamToFastq", "fastqc", + "picard_SamToFastq", "samtools_flagstat" ], "update_time": "2022-03-25", @@ -166737,20 +182069,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -166776,20 +182108,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -166815,20 +182147,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -166854,20 +182186,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -166893,20 +182225,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -166934,8 +182266,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -166963,8 +182295,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -166992,8 +182324,8 @@ "tools": [ "split_file_to_collection", "param_value_from_file", - "fasterq_dump", - "__APPLY_RULES__" + "__APPLY_RULES__", + "fasterq_dump" ], "update_time": "2022-03-18", "versions": 1 @@ -167006,11 +182338,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "1dd4392c51766383", @@ -167026,15 +182358,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167047,11 +182379,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "fe4e34a407157389", @@ -167067,15 +182399,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167087,15 +182419,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "27205feb28b0ce06", @@ -167111,17 +182443,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167133,15 +182465,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "ca7fc6e2adbf1f26", @@ -167159,17 +182491,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167181,15 +182513,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "d3521c05077192df", @@ -167207,17 +182539,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167229,15 +182561,15 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "ba30cc4a84c449f9", @@ -167255,17 +182587,17 @@ "emergen_validated" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2022-03-18", "versions": 1 @@ -167277,14 +182609,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "be9213411c520096", @@ -167301,22 +182633,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167328,14 +182660,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "094a545d44ce28cc", @@ -167352,22 +182684,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167379,14 +182711,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "c1ce3f2ae7c81c3e", @@ -167403,22 +182735,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167430,14 +182762,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "3223ceaa2b58d940", @@ -167454,22 +182786,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167481,14 +182813,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "3c657dd766d02f6a", @@ -167505,22 +182837,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167532,14 +182864,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "810242a3dc4f6170", @@ -167556,22 +182888,22 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", - "tp_replace_in_line", "samtools_stats", "lofreq_viterbi", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "qualimap_bamqc", - "__FLATTEN__", + "vcfvcfintersect", + "tp_replace_in_line", + "lofreq_indelqual", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167583,14 +182915,14 @@ ], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "2b2ce7e1206d177d", @@ -167607,26 +182939,26 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "fastp", "lofreq_call", - "lofreq_indelqual", - "ivar_removereads", - "vcfvcfintersect", - "tp_replace_in_line", - "samtools_stats", - "snpSift_filter", - "__FILTER_FAILED_DATASETS__", - "compose_text_param", "qualimap_bamqc", + "multiqc", "bcftools_annotate", - "__FLATTEN__", - "ivar_trim", - "lofreq_filter", + "lofreq_indelqual", "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "samtools_view", "lofreq_viterbi", - "multiqc" + "compose_text_param", + "tp_replace_in_line", + "vcfvcfintersect", + "snpeff_sars_cov_2", + "samtools_stats", + "lofreq_filter", + "fastp", + "__FILTER_FAILED_DATASETS__", + "ivar_removereads", + "snpSift_filter" ], "update_time": "2022-03-18", "versions": 1 @@ -167638,15 +182970,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "4bc8ac41ecff7daf", @@ -167664,20 +182996,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167689,15 +183021,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "48a60965b6b3ff54", @@ -167715,20 +183047,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167740,15 +183072,15 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "888f8377eb6eabf2", @@ -167766,20 +183098,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", + "snpeff_sars_cov_2", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2022-03-18", "versions": 1 @@ -167791,16 +183123,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "ba7a9d4c857d26b7", @@ -167818,27 +183150,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -167850,16 +183182,16 @@ ], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Sequence contamination filtering", - "Statistical calculation", - "Mapping", - "SNP detection", "Validation", - "Base-calling" + "Mapping", + "SNP detection" ], "edam_topic": [], "id": "932bad88f8dc8d33", @@ -167877,27 +183209,27 @@ "covid19.galaxyproject.org" ], "tools": [ - "snpeff_sars_cov_2", - "samtools_view", - "minimap2", - "fastp", "tp_find_and_replace", - "datamash_ops", - "samtools_stats", - "Add_a_column1", - "bamleftalign", - "__FILTER_FAILED_DATASETS__", - "medaka_variant", - "param_value_from_file", "qualimap_bamqc", + "param_value_from_file", + "Add_a_column1", + "multiqc", + "medaka_consensus", "bcftools_annotate", "__FLATTEN__", - "tp_replace_in_column", "ivar_trim", + "bamleftalign", + "samtools_view", + "tp_replace_in_column", + "snpeff_sars_cov_2", + "minimap2", + "samtools_stats", + "medaka_variant", "lofreq_filter", - "medaka_consensus", - "multiqc", - "bedtools_intersectbed" + "fastp", + "__FILTER_FAILED_DATASETS__", + "bedtools_intersectbed", + "datamash_ops" ], "update_time": "2022-03-18", "versions": 1 @@ -167925,18 +183257,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -167964,18 +183296,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -168003,18 +183335,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -168042,18 +183374,18 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", + "snpSift_extractFields", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "snpSift_extractFields", + "compose_text_param", "Cut1", - "bcftools_consensus", "gops_merge_1", - "compose_text_param", - "Filter1", - "snpSift_filter" + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2022-03-18", "versions": 1 @@ -168076,11 +183408,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "comp1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "comp1", + "datamash_ops" ], "update_time": "2022-03-16", "versions": 0 @@ -168103,10 +183435,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "get_orfs_or_cdss", + "collapse_dataset", "ncbi_acc_download", "jbrowse", - "collapse_dataset" + "get_orfs_or_cdss" ], "update_time": "2022-03-11", "versions": 2 @@ -168129,11 +183461,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "join1", - "datamash_ops", "sort1", "Show beginning1", - "bedtools_intersectbed" + "bedtools_intersectbed", + "join1", + "datamash_ops" ], "update_time": "2022-03-10", "versions": 1 @@ -168156,10 +183488,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "get_orfs_or_cdss", + "collapse_dataset", "ncbi_acc_download", "jbrowse", - "collapse_dataset" + "get_orfs_or_cdss" ], "update_time": "2022-03-09", "versions": 1 @@ -168169,18 +183501,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Scatter plot plotting", - "Read mapping", - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", "Sequence contamination filtering", "Genome assembly", + "Scatter plot plotting", + "Sequence assembly visualisation", + "Sequencing quality control", "Sequence file editing", - "Validation" + "Box-Whisker plot plotting", + "Aggregation", + "Pairwise sequence alignment", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "9c60b83feaa22415", @@ -168196,21 +183528,21 @@ "assembly" ], "tools": [ - "__ZIP_COLLECTION__", - "fasta_filter_by_length", - "collapse_dataset", + "bowtie2", + "samtools_stats", + "bandage_info", "samtools_fastx", - "samtools_view", - "nanoplot", + "collapse_dataset", "seqtk_sample", - "bandage_image", - "minimap2", - "samtools_stats", - "fastp", "multiqc", - "bowtie2", + "fastp", + "nanoplot", + "bandage_image", + "__ZIP_COLLECTION__", "unicycler", - "bandage_info" + "fasta_filter_by_length", + "minimap2", + "samtools_view" ], "update_time": "2022-03-06", "versions": 12 @@ -168220,8 +183552,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence contamination filtering" + "Sequence contamination filtering", + "Sequencing quality control" ], "edam_topic": [], "id": "77951619443e6f87", @@ -168248,9 +183580,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", "Pairwise sequence alignment", - "Sequence file editing" + "Sequence file editing", + "Data handling" ], "edam_topic": [], "id": "324c683a8e2fa5b0", @@ -168279,8 +183611,8 @@ ], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence contamination filtering" + "Sequence contamination filtering", + "Sequencing quality control" ], "edam_topic": [], "id": "c5f000229dd93599", @@ -168307,12 +183639,12 @@ ], "doi": "", "edam_operation": [ - "Box-Whisker plot plotting", - "Scatter plot plotting", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Scatter plot plotting", + "Validation", "Sequencing quality control", - "Validation" + "Box-Whisker plot plotting" ], "edam_topic": [], "id": "3ac73a2f00423326", @@ -168327,9 +183659,9 @@ "lg-wf" ], "tools": [ - "fastqc", "multiqc", - "nanoplot" + "nanoplot", + "fastqc" ], "update_time": "2021-11-09", "versions": 19 @@ -168399,9 +183731,9 @@ ], "doi": "", "edam_operation": [ - "Variant calling", "Sequence assembly", - "Base-calling" + "Base-calling", + "Variant calling" ], "edam_topic": [], "id": "705658f68ae73930", @@ -168416,8 +183748,8 @@ "lg-wf" ], "tools": [ - "medaka_consensus_pipeline", - "fasta-stats" + "fasta-stats", + "medaka_consensus_pipeline" ], "update_time": "2021-11-09", "versions": 51 @@ -168440,8 +183772,8 @@ "lg-wf" ], "tools": [ - "meryl", - "genomescope" + "genomescope", + "meryl" ], "update_time": "2021-11-09", "versions": 4 @@ -168453,10 +183785,10 @@ ], "doi": "", "edam_operation": [ - "Sequence assembly validation", "Visualisation", - "Scaffolding", "Genome assembly", + "Sequence assembly validation", + "Scaffolding", "Transcriptome assembly" ], "edam_topic": [], @@ -168483,10 +183815,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly validation", - "Visualisation", "De-novo assembly", + "Visualisation", "Genome assembly", + "Sequence assembly validation", "Sequence assembly visualisation", "Mapping assembly", "Cross-assembly" @@ -168505,9 +183837,9 @@ ], "tools": [ "flye", + "fasta-stats", "bandage_image", "quast", - "fasta-stats", "barchart_gnuplot" ], "update_time": "2021-11-09", @@ -168556,13 +183888,13 @@ "transcriptomics" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", "scanpy_plot", + "anndata_manipulate", "scanpy_inspect", - "scanpy_filter", "scanpy_normalize", - "scanpy_remove_confounders" + "scanpy_remove_confounders", + "scanpy_filter", + "anndata_inspect" ], "update_time": "2021-10-06", "versions": 20 @@ -168589,16 +183921,16 @@ "transcriptomics" ], "tools": [ - "anndata_inspect", "cat1", - "anndata_manipulate", + "Filter1", "scanpy_plot", - "tp_awk_tool", - "Cut1", + "tp_tail_tool", + "anndata_manipulate", "scanpy_inspect", - "Filter1", "tp_replace_in_column", - "tp_tail_tool" + "Cut1", + "anndata_inspect", + "tp_awk_tool" ], "update_time": "2021-10-06", "versions": 29 @@ -168625,9 +183957,9 @@ "transcriptomics" ], "tools": [ - "scanpy_cluster_reduce_dimension", + "scanpy_plot", "scanpy_inspect", - "scanpy_plot" + "scanpy_cluster_reduce_dimension" ], "update_time": "2021-10-05", "versions": 24 @@ -168654,8 +183986,8 @@ "transcriptomics" ], "tools": [ - "scanpy_cluster_reduce_dimension", - "scanpy_plot" + "scanpy_plot", + "scanpy_cluster_reduce_dimension" ], "update_time": "2021-09-21", "versions": 9 @@ -168680,9 +184012,9 @@ "transcriptomics" ], "tools": [ - "__FILTER_FROM_FILE__", "__EXTRACT_DATASET__", - "anndata_manipulate" + "anndata_manipulate", + "__FILTER_FROM_FILE__" ], "update_time": "2021-09-21", "versions": 13 @@ -168751,12 +184083,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", - "Sequence alignment" + "Sequence alignment", + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "738c0e8227519c25", @@ -168769,12 +184101,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", - "samtools_flagstat", - "snpEff", "freebayes", + "snpEff", + "samtools_idxstats", "vcfallelicprimitives", - "samtools_idxstats" + "bwa_mem", + "samtools_flagstat" ], "update_time": "2021-09-08", "versions": 9 @@ -168784,20 +184116,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Aggregation", + "Sequence contamination filtering", + "Statistical calculation", + "Visualisation", + "Genome assembly", "Scatter plot plotting", - "Sequence composition calculation", "Sequencing quality control", + "Scaffolding", "Box-Whisker plot plotting", + "Transcriptome assembly", + "Aggregation", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Scaffolding", - "Sequence contamination filtering", - "Statistical calculation", - "Genome assembly", "Validation", - "Transcriptome assembly" + "Filtering" ], "edam_topic": [], "id": "b7aa22291322e505", @@ -168810,14 +184142,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "filtlong", - "nanoplot", - "quast", + "fastqc", "fastp", "multiqc", + "nanoplot", + "quast", "busco", - "fastqc", - "unicycler" + "unicycler", + "filtlong" ], "update_time": "2021-08-12", "versions": 13 @@ -168827,21 +184159,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Transcriptome assembly", - "Mapping assembly", - "De-novo assembly", - "Sequence assembly", - "Read mapping", - "Read alignment", - "Sequence alignment", - "Sequence assembly validation", "Visualisation", + "Genome assembly", "Analysis", + "Sequence assembly", + "Mapping assembly", + "Sequence alignment", "Scaffolding", - "Genome assembly", - "Genome indexing", + "Cross-assembly", + "Transcriptome assembly", + "De-novo assembly", "Generation", - "Cross-assembly" + "Genome indexing", + "Read alignment", + "Sequence assembly validation", + "Read mapping" ], "edam_topic": [], "id": "02c74095a7128c9d", @@ -168854,10 +184186,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", + "pilon", "flye", "quast", - "pilon", + "bwa_mem", "busco" ], "update_time": "2021-06-04", @@ -168868,12 +184200,12 @@ "creators": [], "doi": "", "edam_operation": [ + "Generation", "Statistical calculation", - "Read mapping", "Genome indexing", - "Generation", "Sequence alignment", - "Variant calling" + "Variant calling", + "Read mapping" ], "edam_topic": [], "id": "52b6fe5af4911b1a", @@ -168886,10 +184218,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "vcfvcfintersect", "freebayes", - "bwa_mem", "samtools_view", - "vcfvcfintersect" + "bwa_mem" ], "update_time": "2021-05-08", "versions": 1 @@ -168912,8 +184244,8 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffmerge", "hisat2", + "cuffmerge", "cufflinks" ], "update_time": "2021-05-06", @@ -168924,10 +184256,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", - "Sequence alignment", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequence alignment", + "Sequencing quality control" ], "edam_topic": [], "id": "55c4d97a08a5ca09", @@ -168940,9 +184272,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", "hisat2", - "trimmomatic" + "trimmomatic", + "fastqc" ], "update_time": "2021-05-06", "versions": 3 @@ -168952,14 +184284,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Statistical calculation", "Differential gene expression analysis", - "Sequencing quality control", "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", + "RNA-Seq quantification", "Read summarisation", - "Statistical calculation", - "RNA-Seq analysis", - "RNA-Seq quantification" + "RNA-Seq analysis" ], "edam_topic": [], "id": "0fc7c14c4d1ac8f5", @@ -168972,11 +184304,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "edger", "fastq_quality_trimmer", + "edger", "featurecounts", - "hisat2", "fastqc", + "hisat2", "deseq2" ], "update_time": "2021-05-06", @@ -169002,10 +184334,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "htseq_count", "generate_count_matrix", "hisat2", - "jbrowse", - "htseq_count" + "jbrowse" ], "update_time": "2021-05-06", "versions": 7 @@ -169015,17 +184347,17 @@ "creators": [], "doi": "", "edam_operation": [ + "Statistical calculation", + "Nucleic acid sequence analysis", + "Sequence alignment", + "Sequencing quality control", + "Transcriptome assembly", "Sequence composition calculation", + "Generation", + "Genome indexing", "Read mapping", - "Sequencing quality control", - "Sequence alignment", - "Nucleic acid sequence analysis", "Genome visualisation", - "Statistical calculation", - "RNA-Seq analysis", - "Genome indexing", - "Generation", - "Transcriptome assembly" + "RNA-Seq analysis" ], "edam_topic": [], "id": "a35e5a238a70176a", @@ -169038,15 +184370,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "htseq_count", "bowtie2", "trimmomatic", - "bwa", + "jbrowse", "stringtie_merge", - "htseq_count", "hisat2", - "jbrowse", "fastqc", - "stringtie" + "stringtie", + "bwa" ], "update_time": "2021-05-05", "versions": 2 @@ -169056,9 +184388,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "2a97585556d53a43", @@ -169071,9 +184403,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", "trimmomatic", "tophat2", - "cufflinks", "fastqc", "cuffmerge" ], @@ -169085,8 +184417,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Nucleic acid sequence analysis" + "Nucleic acid sequence analysis", + "Genome visualisation" ], "edam_topic": [], "id": "b2818098da6e2f82", @@ -169100,9 +184432,9 @@ "tags": [], "tools": [ "htseq_count", + "cufflinks", "tophat2", "jbrowse", - "cufflinks", "cuffmerge" ], "update_time": "2021-05-04", @@ -169113,12 +184445,12 @@ "creators": [], "doi": "", "edam_operation": [ + "Pairwise sequence alignment", "Filtering", + "Sequence analysis", "Scatter plot plotting", "Structural variation detection", - "Sequence analysis", "Sequencing quality control", - "Pairwise sequence alignment", "Formatting", "Box-Whisker plot plotting" ], @@ -169136,14 +184468,14 @@ ], "tools": [ "samtools_calmd", + "vcfsort", + "samtools_idxstats", + "nanoplot", "tp_awk_tool", + "picard_SortSam", "filtlong", - "nanoplot", - "sniffles", "minimap2", - "picard_SortSam", - "samtools_idxstats", - "vcfsort" + "sniffles" ], "update_time": "2021-04-28", "versions": 43 @@ -169153,24 +184485,24 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence assembly", - "Read alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", + "Gene prediction", + "Genome annotation", "Genome assembly", + "Analysis", + "Sequence assembly visualisation", + "Sequence assembly", "Mapping assembly", - "Genome indexing", - "Generation", - "Cross-assembly", "Scatter plot plotting", - "Read mapping", "Sequence alignment", - "Genome visualisation", - "Gene prediction", - "Analysis", - "Genome annotation", - "Coding region prediction" + "Cross-assembly", + "Box-Whisker plot plotting", + "Coding region prediction", + "De-novo assembly", + "Generation", + "Genome indexing", + "Read alignment", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "7c343e5b55474d19", @@ -169185,15 +184517,15 @@ "assembly" ], "tools": [ - "bwa_mem", - "flye", - "bandage_image", - "nanoplot", - "fasta-stats", "pilon", - "jbrowse", + "bandage_info", + "flye", "prokka", - "bandage_info" + "fasta-stats", + "nanoplot", + "bandage_image", + "bwa_mem", + "jbrowse" ], "update_time": "2021-04-15", "versions": 20 @@ -169203,13 +184535,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree reconstruction", + "Pairwise sequence alignment", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment", + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree analysis", - "Pairwise sequence alignment", - "Phylogenetic tree generation" + "Multiple sequence alignment" ], "edam_topic": [], "id": "a01c3004bcef9dd3", @@ -169223,9 +184555,9 @@ "tags": [], "tools": [ "minimap2", + "rbc_mafft", "fasttree", - "newick_display", - "rbc_mafft" + "newick_display" ], "update_time": "2021-04-14", "versions": 6 @@ -169251,13 +184583,13 @@ ], "tools": [ "symmetricPlot", + "phyloseq_DESeq2", "phyloseq_abundance", - "phyloseq_richness", + "phyloseq_net", "biom_add_metadata", - "biom_convert", "phyloseq_taxonomy", - "phyloseq_DESeq2", - "phyloseq_net" + "phyloseq_richness", + "biom_convert" ], "update_time": "2021-04-01", "versions": 9 @@ -169268,15 +184600,15 @@ "doi": "", "edam_operation": [ "DNA mapping", + "Statistical calculation", + "Sequence alignment", "Chimera detection", - "Sequence composition calculation", - "Read mapping", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping" ], "edam_topic": [], "id": "869440d35a618836", @@ -169291,28 +184623,28 @@ "metadegalaxy" ], "tools": [ - "vsearch_search", - "vsearch_chimera_detection", - "vsearch_clustering", - "biom_convert", - "phyloseq_DESeq2", + "trimmomatic", "fastqc", "phyloseq_richness", - "phyloseq_taxonomy", - "vsearch_dereplication", - "uclust2otutable", - "samtools_fastx", + "symmetricPlot", + "vsearch_chimera_detection", + "phyloseq_net", "biom_add_metadata", - "cat_multi_datasets", + "bwa_mem", "addValue", - "picard_FilterSamReads", "cat1", - "bwa_mem", - "symmetricPlot", - "trimmomatic", - "Cut1", + "samtools_fastx", "phyloseq_abundance", - "phyloseq_net" + "uclust2otutable", + "vsearch_clustering", + "phyloseq_DESeq2", + "picard_FilterSamReads", + "vsearch_search", + "cat_multi_datasets", + "phyloseq_taxonomy", + "Cut1", + "biom_convert", + "vsearch_dereplication" ], "update_time": "2021-04-01", "versions": 18 @@ -169323,16 +184655,16 @@ "doi": "", "edam_operation": [ "DNA mapping", + "Statistical calculation", + "Sequence alignment", "Chimera detection", - "Sequence merging", - "Sequence composition calculation", - "Read mapping", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Statistical calculation", + "Sequence composition calculation", + "Generation", "Genome indexing", - "Generation" + "Read mapping", + "Sequence merging" ], "edam_topic": [], "id": "14e80b7f9f68ec2a", @@ -169347,29 +184679,29 @@ "metadegalaxy" ], "tools": [ - "vsearch_search", - "vsearch_chimera_detection", - "vsearch_clustering", - "biom_convert", - "iuc_pear", - "picard_MergeSamFiles", - "phyloseq_DESeq2", + "trimmomatic", "fastqc", "phyloseq_richness", - "phyloseq_taxonomy", - "vsearch_dereplication", - "uclust2otutable", - "samtools_fastx", + "symmetricPlot", + "vsearch_chimera_detection", + "phyloseq_net", + "picard_MergeSamFiles", "biom_add_metadata", + "iuc_pear", + "bwa_mem", "addValue", - "picard_FilterSamReads", "cat1", - "bwa_mem", - "symmetricPlot", - "trimmomatic", - "Cut1", + "samtools_fastx", "phyloseq_abundance", - "phyloseq_net" + "uclust2otutable", + "vsearch_clustering", + "phyloseq_DESeq2", + "picard_FilterSamReads", + "vsearch_search", + "phyloseq_taxonomy", + "Cut1", + "biom_convert", + "vsearch_dereplication" ], "update_time": "2021-04-01", "versions": 16 @@ -169379,14 +184711,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", + "Pairwise sequence alignment", + "Sequence analysis", "Scatter plot plotting", "Structural variation detection", - "Sequence visualisation", - "Sequence analysis", "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting" + "Filtering", + "Box-Whisker plot plotting", + "Sequence visualisation" ], "edam_topic": [], "id": "4871f853090e8be8", @@ -169401,17 +184733,17 @@ "sv_calling" ], "tools": [ - "vcfannotate", "samtools_calmd", - "tp_awk_tool", - "filtlong", - "tab2fasta", - "nanoplot", "sniffles", - "minimap2", + "vcfsort", "Extract_features1", + "tab2fasta", + "nanoplot", "circos", - "vcfsort" + "filtlong", + "minimap2", + "tp_awk_tool", + "vcfannotate" ], "update_time": "2021-03-22", "versions": 48 @@ -169436,8 +184768,8 @@ "sv_calling" ], "tools": [ - "tp_awk_tool", - "circos" + "circos", + "tp_awk_tool" ], "update_time": "2021-03-22", "versions": 21 @@ -169460,9 +184792,9 @@ "sv_calling" ], "tools": [ + "vcfannotate", "tp_awk_tool", - "Extract_features1", - "vcfannotate" + "Extract_features1" ], "update_time": "2021-03-21", "versions": 23 @@ -169472,8 +184804,8 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", - "Annotation" + "Annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "bdb498b1f0e8944f", @@ -169490,8 +184822,8 @@ ], "tools": [ "limma_voom", - "tp_cut_tool", "tp_replace_in_line", + "tp_cut_tool", "annotatemyids", "mergeCols1" ], @@ -169517,8 +184849,8 @@ "galaxy-training-network" ], "tools": [ - "__FLATTEN__", - "collection_column_join" + "collection_column_join", + "__FLATTEN__" ], "update_time": "2021-03-19", "versions": 0 @@ -169528,17 +184860,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "a763e53653b10ce0", @@ -169554,14 +184886,14 @@ "galaxy-training-network" ], "tools": [ - "tp_sort_header_tool", - "rna_star", "featurecounts", - "rseqc_infer_experiment", - "gtftobed12", "multiqc", + "gtftobed12", + "tp_sort_header_tool", "fastqc", - "cutadapt" + "rna_star", + "cutadapt", + "rseqc_infer_experiment" ], "update_time": "2021-03-19", "versions": 0 @@ -169571,11 +184903,11 @@ "creators": [], "doi": "", "edam_operation": [ + "Gene functional annotation", + "Differential gene expression analysis", "Pathway or network analysis", "Pathway or network visualisation", - "RNA-Seq analysis", - "Differential gene expression analysis", - "Gene functional annotation" + "RNA-Seq analysis" ], "edam_topic": [], "id": "5490661d0153962b", @@ -169591,19 +184923,19 @@ "galaxy-training-network" ], "tools": [ + "pathview", "cat1", - "ggplot2_heatmap2", + "Filter1", "Add_a_column1", - "pathview", + "goseq", "table_compute", - "Cut1", - "join1", - "Filter1", "ChangeCase", - "Grouping1", "deg_annotate", - "deseq2", - "goseq" + "Grouping1", + "join1", + "Cut1", + "ggplot2_heatmap2", + "deseq2" ], "update_time": "2021-03-19", "versions": 0 @@ -169613,8 +184945,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Gene set testing", "Gene functional annotation", + "Gene set testing", "Gene-set enrichment analysis" ], "edam_topic": [], @@ -169631,13 +184963,13 @@ "galaxy-training-network" ], "tools": [ + "fgsea", "Add_a_column1", - "egsea", "tp_sort_header_tool", + "egsea", + "join1", "tp_cut_tool", "Cut1", - "join1", - "fgsea", "goseq" ], "update_time": "2021-03-19", @@ -169648,18 +184980,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Formatting", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Read summarisation", + "Formatting", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", + "RNA-Seq quantification", "Validation", - "RNA-Seq quantification" + "Data handling" ], "edam_topic": [], "id": "af7b95f46485308c", @@ -169675,17 +185007,17 @@ "galaxy-training-network" ], "tools": [ - "picard_MarkDuplicates", - "rseqc_read_distribution", + "rseqc_geneBody_coverage", "featurecounts", - "rseqc_infer_experiment", - "hisat2", + "samtools_idxstats", + "cutadapt", "multiqc", - "rseqc_geneBody_coverage", "collection_column_join", "fastqc", - "samtools_idxstats", - "cutadapt" + "hisat2", + "rseqc_infer_experiment", + "rseqc_read_distribution", + "picard_MarkDuplicates" ], "update_time": "2021-03-19", "versions": 0 @@ -169695,16 +185027,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence annotation", - "Sequencing quality control", - "Differential gene expression analysis", - "Sequence alignment", - "Read summarisation", "Statistical calculation", + "Sequence alignment", + "Differential gene expression analysis", + "Sequencing quality control", "Transcriptome assembly", - "RNA-Seq analysis", - "RNA-Seq quantification" + "Sequence composition calculation", + "RNA-Seq quantification", + "Read summarisation", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "53010c2f1f207429", @@ -169720,16 +185052,16 @@ "galaxy-training-network" ], "tools": [ - "deeptools_bam_coverage", - "gffcompare", + "Filter1", + "featurecounts", "trimmomatic", "stringtie_merge", - "featurecounts", - "Filter1", - "hisat2", + "deeptools_bam_coverage", "fastqc", - "deseq2", - "stringtie" + "gffcompare", + "stringtie", + "hisat2", + "deseq2" ], "update_time": "2021-03-19", "versions": 0 @@ -169763,13 +185095,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment" + "Statistical calculation", + "Sequence alignment", + "Sequence trimming", + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "5926a7669eabb1c6", @@ -169785,12 +185117,12 @@ "galaxy-training-network" ], "tools": [ + "samtool_filter2", "trim_galore", "bedtools_bamtofastq", - "samtool_filter2", - "hisat2", + "fastq_manipulation", "fastqc", - "fastq_manipulation" + "hisat2" ], "update_time": "2021-03-19", "versions": 0 @@ -169801,10 +185133,10 @@ "doi": "", "edam_operation": [ "Sequence composition calculation", - "RNA-Seq analysis", - "Differential gene expression analysis", "Gene expression analysis", - "RNA-Seq quantification" + "Differential gene expression analysis", + "RNA-Seq quantification", + "RNA-Seq analysis" ], "edam_topic": [], "id": "3f45685df9b9e792", @@ -169820,9 +185152,9 @@ "galaxy-training-network" ], "tools": [ + "Filter1", "salmon", - "deseq2", - "Filter1" + "deseq2" ], "update_time": "2021-03-19", "versions": 0 @@ -169846,10 +185178,10 @@ "galaxy-training-network" ], "tools": [ - "samtools_sort", - "blockclust", + "blockbuster", "tp_sort_header_tool", - "blockbuster" + "samtools_sort", + "blockclust" ], "update_time": "2021-03-19", "versions": 0 @@ -169859,9 +185191,9 @@ "creators": [], "doi": "", "edam_operation": [ - "RNA-Seq analysis", "Pathway or network analysis", - "Differential gene expression analysis" + "Differential gene expression analysis", + "RNA-Seq analysis" ], "edam_topic": [], "id": "6a161c87d19a543c", @@ -169877,12 +185209,12 @@ "galaxy-training-network" ], "tools": [ + "heinz_scoring", "heinz_bum", + "heinz", "heinz_visualization", "Cut1", - "heinz", - "deseq2", - "heinz_scoring" + "deseq2" ], "update_time": "2021-03-19", "versions": 0 @@ -169906,10 +185238,10 @@ "galaxy-training-network" ], "tools": [ - "join1", - "datamash_transpose", + "Cut1", "ggplot2_heatmap2", - "Cut1" + "datamash_transpose", + "join1" ], "update_time": "2021-03-19", "versions": 0 @@ -169935,8 +185267,8 @@ "galaxy-training-network" ], "tools": [ - "Filter1", "goslimmer", + "Filter1", "goenrichment" ], "update_time": "2021-03-19", @@ -169947,13 +185279,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", - "Sequence composition calculation", - "Primer removal", "Read pre-processing", + "Sequence composition calculation", + "Statistical calculation", + "Validation", "Sequence trimming", - "Sequencing quality control", - "Validation" + "Primer removal", + "Sequencing quality control" ], "edam_topic": [], "id": "7ba13e928de65e61", @@ -169969,9 +185301,9 @@ "galaxy-training-network" ], "tools": [ - "fastqc", + "cutadapt", "multiqc", - "cutadapt" + "fastqc" ], "update_time": "2021-03-19", "versions": 0 @@ -169981,16 +185313,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", + "Sequence alignment analysis", "Sequence trimming", - "Statistical calculation", - "Validation" + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "0a477899db53d098", @@ -170006,12 +185338,12 @@ "galaxy-training-network" ], "tools": [ - "bamFilter", - "trim_galore", + "bowtie2", "samtools_stats", "multiqc", + "trim_galore", "fastqc", - "bowtie2" + "bamFilter" ], "update_time": "2021-03-19", "versions": 0 @@ -170021,15 +185353,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Genome visualisation", + "Statistical calculation", "Primer removal", + "Sequencing quality control", "Read pre-processing", + "Sequence composition calculation", "Sequence trimming", - "Statistical calculation", - "Validation" + "Validation", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "c456492ce4f963d0", @@ -170045,12 +185377,12 @@ "galaxy-training-network" ], "tools": [ - "trim_galore", + "bowtie2", "samtools_stats", "multiqc", - "jbrowse", + "trim_galore", "fastqc", - "bowtie2" + "jbrowse" ], "update_time": "2021-03-19", "versions": 0 @@ -170060,13 +185392,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "2a6324600f159061", @@ -170083,11 +185415,11 @@ ], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_sub_sample", "mothur_classify_otu", - "mothur_count_groups", - "mothur_remove_groups" + "mothur_remove_groups", + "mothur_sub_sample", + "mothur_cluster_split", + "mothur_count_groups" ], "update_time": "2021-03-19", "versions": 0 @@ -170097,13 +185429,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "58bd08b1530e7cae", @@ -170120,8 +185452,8 @@ ], "tools": [ "mothur_make_shared", - "mothur_rarefaction_single", "mothur_cluster", + "mothur_rarefaction_single", "mothur_dist_seqs" ], "update_time": "2021-03-19", @@ -170132,13 +185464,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "7e381c150820e506", @@ -170154,9 +185486,9 @@ "galaxy-training-network" ], "tools": [ - "mothur_remove_lineage", "mothur_summary_seqs", - "mothur_classify_seqs" + "mothur_classify_seqs", + "mothur_remove_lineage" ], "update_time": "2021-03-19", "versions": 0 @@ -170166,13 +185498,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "1954437da1e0c4de", @@ -170188,8 +185520,8 @@ "galaxy-training-network" ], "tools": [ - "mothur_summary_seqs", "mothur_count_seqs", + "mothur_summary_seqs", "mothur_unique_seqs", "mothur_screen_seqs" ], @@ -170201,13 +185533,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "832fe9dfc67fd8ed", @@ -170225,11 +185557,11 @@ "tools": [ "mothur_pre_cluster", "mothur_screen_seqs", - "mothur_remove_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", - "mothur_summary_seqs" + "mothur_filter_seqs", + "mothur_remove_seqs", + "mothur_unique_seqs" ], "update_time": "2021-03-19", "versions": 0 @@ -170239,13 +185571,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "5877e2d5eba79f36", @@ -170273,16 +185605,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "a52609119b30e64d", @@ -170298,11 +185630,11 @@ "galaxy-training-network" ], "tools": [ + "mothur_dist_shared", + "mothur_tree_shared", + "collapse_dataset", "mothur_venn", "mothur_heatmap_sim", - "collapse_dataset", - "mothur_tree_shared", - "mothur_dist_shared", "newick_display" ], "update_time": "2021-03-19", @@ -170313,14 +185645,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Sequence similarity search", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence comparison", "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence comparison", + "Sequence similarity search", + "Sequence composition calculation", "Read pre-processing", + "Sequence alignment analysis", "Sequence trimming", "Validation" ], @@ -170339,8 +185671,8 @@ ], "tools": [ "bg_sortmerna", - "fastq_paired_end_interlacer", "multiqc", + "fastq_paired_end_interlacer", "fastqc", "cutadapt" ], @@ -170352,16 +185684,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Phylogenetic tree analysis", + "Visualisation", + "Sequence clustering", + "Phylogenetic tree generation", + "DNA barcoding", "Sequencing quality control", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation", - "Visualisation", "Phylogenetic tree reconstruction", - "Sequence clustering", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "2717e90438c7fb8c", @@ -170377,39 +185709,39 @@ "galaxy-training-network" ], "tools": [ - "mothur_cluster_split", "mothur_screen_seqs", - "mothur_count_seqs", + "mothur_sub_sample", + "mothur_cluster", + "mothur_make_biom", + "newick_display", + "mothur_count_groups", + "mothur_classify_seqs", "mothur_dist_shared", + "mothur_tree_shared", + "mothur_remove_lineage", + "mothur_taxonomy_to_krona", + "mothur_seq_error", + "mothur_unique_seqs", "mothur_classify_otu", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_venn", "taxonomy_krona_chart", - "mothur_count_groups", - "mothur_make_contigs", - "mothur_make_biom", - "mothur_make_shared", - "mothur_pre_cluster", + "mothur_filter_seqs", + "mothur_remove_seqs", "mothur_summary_single", - "mothur_taxonomy_to_krona", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_make_shared", "mothur_remove_groups", - "mothur_venn", - "mothur_sub_sample", - "mothur_classify_seqs", - "mothur_filter_seqs", - "mothur_chimera_vsearch", - "mothur_summary_seqs", - "newick_display", - "mothur_rarefaction_single", + "mothur_pre_cluster", "mothur_get_groups", - "mothur_align_seqs", + "mothur_chimera_vsearch", "mothur_heatmap_sim", - "mothur_remove_lineage", - "mothur_tree_shared", - "mothur_remove_seqs", - "mothur_cluster", - "mothur_unique_seqs", + "mothur_rarefaction_single", + "mothur_make_contigs", "mothur_dist_seqs", - "XY_Plot_1", - "mothur_seq_error" + "XY_Plot_1" ], "update_time": "2021-03-19", "versions": 0 @@ -170419,13 +185751,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "74bd939615090c2c", @@ -170442,20 +185774,20 @@ ], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "krona-text", - "mothur_pre_cluster", - "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", - "mothur_make_group", "mothur_classify_otu", + "mothur_make_group", + "mothur_screen_seqs", + "mothur_pre_cluster", "mothur_summary_seqs", - "mothur_merge_files", + "mothur_align_seqs", + "mothur_filter_seqs", "mothur_make_biom", - "mothur_align_seqs" + "krona-text", + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2021-03-19", "versions": 0 @@ -170479,18 +185811,18 @@ "galaxy-training-network" ], "tools": [ - "cardinal_preprocessing", - "cardinal_mz_images", + "Filter1", + "join_files_on_column_fuzzy", "cardinal_classification", - "cardinal_combine", - "Grep1", - "Summary_Statistics1", - "maldi_quant_preprocessing", "cardinal_segmentations", "maldi_quant_peak_detection", - "join_files_on_column_fuzzy", - "Filter1", - "cardinal_quality_report" + "cardinal_mz_images", + "Grep1", + "maldi_quant_preprocessing", + "cardinal_quality_report", + "Summary_Statistics1", + "cardinal_combine", + "cardinal_preprocessing" ], "update_time": "2021-03-19", "versions": 0 @@ -170500,13 +185832,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "fa0243ff9b5ca997", @@ -170522,19 +185854,19 @@ "galaxy-training-network" ], "tools": [ - "xcms_merge", + "wsdl_hmdb", + "abims_xcms_xcmsSet", + "generic_filter", + "abims_xcms_retcor", + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "Univariate", + "abims_xcms_group", "abims_xcms_fillPeaks", + "xcms_merge", "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", - "abims_xcms_xcmsSet", - "Batch_correction", - "wsdl_hmdb", "quality_metrics", - "Univariate", - "xcms_plot_chromatogram", - "abims_xcms_retcor", - "generic_filter", - "abims_xcms_group" + "Batch_correction" ], "update_time": "2021-03-19", "versions": 0 @@ -170585,8 +185917,8 @@ "galaxy-training-network" ], "tools": [ - "Filter1", "gops_intersect_1", + "Filter1", "tp_cat" ], "update_time": "2021-03-19", @@ -170613,13 +185945,13 @@ "galaxy-training-network" ], "tools": [ - "ggplot2_point", "Cut1", "tp_sorted_uniq", - "datamash_ops", "Remove beginning1", + "Grouping1", "csv_to_tabular", - "Grouping1" + "ggplot2_point", + "datamash_ops" ], "update_time": "2021-03-19", "versions": 0 @@ -170629,9 +185961,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b46bc04e0418fdfa", @@ -170647,8 +185979,8 @@ "galaxy-training-network" ], "tools": [ - "fastqc", - "cshl_fastq_quality_filter" + "cshl_fastq_quality_filter", + "fastqc" ], "update_time": "2021-03-19", "versions": 0 @@ -170682,9 +186014,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", "Coding region prediction", + "Genome visualisation", "Genome annotation" ], "edam_topic": [], @@ -170701,8 +186033,8 @@ "galaxy-training-network" ], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2021-03-19", "versions": 0 @@ -170799,8 +186131,8 @@ "galaxy-training-network" ], "tools": [ - "Filter1", - "Paste1" + "Paste1", + "Filter1" ], "update_time": "2021-03-19", "versions": 0 @@ -170824,8 +186156,8 @@ "galaxy-training-network" ], "tools": [ - "Filter1", - "Paste1" + "Paste1", + "Filter1" ], "update_time": "2021-03-19", "versions": 0 @@ -170835,12 +186167,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Primer removal", "Read pre-processing", "Sequence trimming", + "Primer removal", "Read mapping", - "Sequence file editing" + "Sequence file editing", + "Data handling" ], "edam_topic": [], "id": "79ca45e45d76871f", @@ -170856,18 +186188,18 @@ "galaxy-training-network" ], "tools": [ - "seqtk_subseq", - "tp_cut_tool", - "Cut1", - "tp_sorted_uniq", - "tp_sed_tool", + "bowtie2", "fastq_to_tabular", + "Filter1", + "Cut1", + "seqtk_subseq", + "bam_to_sam", "tp_cat", "random_lines1", - "Filter1", - "bowtie2", - "cutadapt", - "bam_to_sam" + "tp_sed_tool", + "tp_cut_tool", + "tp_sorted_uniq", + "cutadapt" ], "update_time": "2021-03-19", "versions": 0 @@ -170891,15 +186223,15 @@ "galaxy-training-network" ], "tools": [ - "rdock_rbcavity", - "collapse_dataset", "rdock_rbdock", - "enumerate_charges", - "ctb_frankenstein_ligand", + "sucos_max_score", "xchem_pose_scoring", - "openbabel_compound_convert", + "collapse_dataset", + "ctb_frankenstein_ligand", + "enumerate_charges", + "rdock_rbcavity", "split_file_to_collection", - "sucos_max_score" + "openbabel_compound_convert" ], "update_time": "2021-03-19", "versions": 0 @@ -170909,18 +186241,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Scatter plot plotting", - "Read mapping", - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", "Sequence contamination filtering", "Genome assembly", + "Scatter plot plotting", + "Sequence assembly visualisation", + "Sequencing quality control", "Sequence file editing", - "Validation" + "Box-Whisker plot plotting", + "Aggregation", + "Pairwise sequence alignment", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "fc3c83b11f527977", @@ -170936,22 +186268,22 @@ "galaxy-training-network" ], "tools": [ - "__ZIP_COLLECTION__", - "fasta_filter_by_length", - "collapse_dataset", + "bowtie2", + "samtools_stats", + "bandage_info", "samtools_fastx", - "samtools_view", - "nanoplot", - "fasterq_dump", + "collapse_dataset", "seqtk_sample", - "bandage_image", - "minimap2", - "samtools_stats", - "fastp", "multiqc", - "bowtie2", + "fastp", + "fasterq_dump", + "nanoplot", + "bandage_image", + "__ZIP_COLLECTION__", "unicycler", - "bandage_info" + "fasta_filter_by_length", + "minimap2", + "samtools_view" ], "update_time": "2021-03-19", "versions": 0 @@ -170961,18 +186293,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Data handling", - "Scatter plot plotting", - "Read mapping", - "Sequencing quality control", - "Pairwise sequence alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", "Sequence contamination filtering", "Genome assembly", + "Scatter plot plotting", + "Sequence assembly visualisation", + "Sequencing quality control", "Sequence file editing", - "Validation" + "Box-Whisker plot plotting", + "Aggregation", + "Pairwise sequence alignment", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "b59fada651043735", @@ -170988,21 +186320,21 @@ "galaxy-training-network" ], "tools": [ - "__ZIP_COLLECTION__", - "fasta_filter_by_length", - "collapse_dataset", + "bowtie2", + "samtools_stats", + "bandage_info", "samtools_fastx", - "samtools_view", - "nanoplot", + "collapse_dataset", "seqtk_sample", - "bandage_image", - "minimap2", - "samtools_stats", - "fastp", "multiqc", - "bowtie2", + "fastp", + "nanoplot", + "bandage_image", + "__ZIP_COLLECTION__", "unicycler", - "bandage_info" + "fasta_filter_by_length", + "minimap2", + "samtools_view" ], "update_time": "2021-03-19", "versions": 0 @@ -171028,11 +186360,11 @@ "galaxy-training-network" ], "tools": [ - "Cut1", - "Remove beginning1", + "Grep1", "random_lines1", + "Remove beginning1", "circos", - "Grep1" + "Cut1" ], "update_time": "2021-03-19", "versions": 0 @@ -171068,17 +186400,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "3e6f755ee62f7301", @@ -171094,16 +186426,16 @@ "galaxy-training-network" ], "tools": [ - "bwa_mem", - "bamleftalign", - "picard_MarkDuplicates", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "Cut1", - "freebayes", + "vcf2tsv", + "bwa_mem", "fastqc", "bamFilter", - "vcf2tsv" + "Cut1", + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2021-03-19", "versions": 0 @@ -171113,10 +186445,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Validation", "Sequencing quality control", "Formatting", - "Validation" + "Data handling" ], "edam_topic": [], "id": "b08342866a118a5e", @@ -171132,10 +186464,10 @@ "galaxy-training-network" ], "tools": [ - "samtools_idxstats", - "picard_MarkDuplicates", + "rseqc_infer_experiment", "multiqc", - "rseqc_infer_experiment" + "samtools_idxstats", + "picard_MarkDuplicates" ], "update_time": "2021-03-19", "versions": 0 @@ -171145,11 +186477,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Loading", - "Community profiling", - "Sequencing quality control", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Community profiling", + "Loading" ], "edam_topic": [], "id": "f627023a3401bf9b", @@ -171195,11 +186527,11 @@ "galaxy-training-network" ], "tools": [ - "search_gui", - "peptide_shaker", + "sqlite_to_tabular", "unipept", + "search_gui", "query_tabular", - "sqlite_to_tabular" + "peptide_shaker" ], "update_time": "2021-03-19", "versions": 0 @@ -171223,16 +186555,16 @@ "galaxy-training-network" ], "tools": [ - "IDScoreSwitcher", - "XTandemAdapter", "FalseDiscoveryRate", - "FidoAdapter", + "IDPosteriorErrorProbability", "PeptideIndexer", + "PeakPickerHiRes", + "Grep1", + "FidoAdapter", "TextExporter", "FileInfo", - "IDPosteriorErrorProbability", - "Grep1", - "PeakPickerHiRes" + "XTandemAdapter", + "IDScoreSwitcher" ], "update_time": "2021-03-19", "versions": 0 @@ -171242,16 +186574,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "f8183bba3a1d150d", @@ -171267,12 +186599,12 @@ "galaxy-training-network" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2021-03-19", "versions": 0 @@ -171282,8 +186614,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Conversion", - "Peptide database search" + "Peptide database search", + "Conversion" ], "edam_topic": [], "id": "1b9bfe7ce484fdc2", @@ -171299,11 +186631,11 @@ "galaxy-training-network" ], "tools": [ - "search_gui", - "peptide_shaker", + "mz_to_sqlite", "tab2fasta", + "search_gui", "query_tabular", - "mz_to_sqlite" + "peptide_shaker" ], "update_time": "2021-03-19", "versions": 0 @@ -171313,12 +186645,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Variant calling", "Statistical calculation", - "Sequence annotation", - "RNA-Seq analysis", + "Transcriptome assembly", + "Variant calling", "Sequence alignment", - "Transcriptome assembly" + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "7cd4fcc8e06ce4fd", @@ -171334,23 +186666,23 @@ "galaxy-training-network" ], "tools": [ - "gffcompare", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", "regexColumn1", - "tab2fasta", - "translate_bed", + "gffcompare", + "filter_tabular", "freebayes", - "bed_to_protein_map", - "hisat2", "gffcompare_to_bed", "query_tabular", - "filter_tabular", "sqlite_to_tabular", - "stringtie", + "tab2fasta", + "fasta2tab", + "tp_cat", + "translate_bed", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "custom_pro_db", - "tp_cat" + "stringtie", + "hisat2", + "bed_to_protein_map" ], "update_time": "2021-03-19", "versions": 0 @@ -171360,17 +186692,17 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", + "Differential protein expression profiling", "Clustering", + "Standardisation and normalisation", "Spectrum calculation", + "Principal component plotting", "Heat map generation", "Protein quantification", "Imputation", - "Tag-based peptide identification", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Differential protein expression profiling", - "Principal component plotting" + "Tag-based peptide identification" ], "edam_topic": [], "id": "1727d16fa4dec19c", @@ -171386,20 +186718,20 @@ "galaxy-training-network" ], "tools": [ - "tp_easyjoin_tool", - "ggplot2_heatmap2", "cat1", + "ggplot2_heatmap", + "msstats", + "Filter1", + "Cut1", + "uniprot", "fasta2tab", "Grep1", - "Summary_Statistics1", - "Cut1", - "datamash_ops", "Remove beginning1", - "uniprot", - "msstats", - "ggplot2_heatmap", - "Filter1", + "Summary_Statistics1", + "tp_easyjoin_tool", "tp_replace_in_column", + "datamash_ops", + "ggplot2_heatmap2", "maxquant" ], "update_time": "2021-03-19", @@ -171424,12 +186756,12 @@ "galaxy-training-network" ], "tools": [ + "tab2fasta", "fasta2tab", "fasta_merge_files_and_filter_unique_sequences", - "DecoyDatabase", - "tab2fasta", + "dbbuilder", "addValue", - "dbbuilder" + "DecoyDatabase" ], "update_time": "2021-03-19", "versions": 0 @@ -171453,12 +186785,12 @@ "galaxy-training-network" ], "tools": [ + "tab2fasta", "fasta2tab", "fasta_merge_files_and_filter_unique_sequences", - "DecoyDatabase", - "tab2fasta", + "dbbuilder", "addValue", - "dbbuilder" + "DecoyDatabase" ], "update_time": "2021-03-19", "versions": 0 @@ -171482,23 +186814,23 @@ "galaxy-training-network" ], "tools": [ - "IDScoreSwitcher", - "XTandemAdapter", "FeatureFinderMultiplex", - "Summary_Statistics1", "FalseDiscoveryRate", + "histogram_rpy", + "IDPosteriorErrorProbability", + "PeptideIndexer", + "tp_tail_tool", + "MultiplexResolver", + "ProteinQuantifier", + "Grep1", + "Summary_Statistics1", "FidoAdapter", "IDConflictResolver", - "MultiplexResolver", - "PeptideIndexer", + "IDMapper", "TextExporter", - "ProteinQuantifier", "FileInfo", - "histogram_rpy", - "IDMapper", - "IDPosteriorErrorProbability", - "Grep1", - "tp_tail_tool" + "XTandemAdapter", + "IDScoreSwitcher" ], "update_time": "2021-03-19", "versions": 0 @@ -171508,16 +186840,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Heat map generation", - "Statistical inference", - "Principal component visualisation", "Visualisation", - "Query and retrieval", + "Indexing", "Differential protein expression analysis", - "Filtering", + "Statistical inference", + "Functional clustering", + "Query and retrieval", "Quantification", - "Indexing", - "Functional clustering" + "Principal component visualisation", + "Heat map generation", + "Filtering" ], "edam_topic": [], "id": "cada735fa0716570", @@ -171533,12 +186865,12 @@ "galaxy-training-network" ], "tools": [ - "metaquantome_viz", - "metaquantome_stat", "metaquantome_expand", + "metaquantome_stat", "metaquantome_sample", - "metaquantome_db", - "metaquantome_filter" + "metaquantome_filter", + "metaquantome_viz", + "metaquantome_db" ], "update_time": "2021-03-19", "versions": 0 @@ -171548,14 +186880,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "781457327e644c7e", @@ -171571,12 +186903,12 @@ "galaxy-training-network" ], "tools": [ + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "Cut1", "histogram_rpy", - "Filter1", "Grep1", + "tp_sort_header_tool", + "Cut1", "maxquant" ], "update_time": "2021-03-19", @@ -171601,10 +186933,10 @@ "galaxy-training-network" ], "tools": [ - "pep_pointer", + "peptide_genomic_coordinate", "query_tabular", "ncbi_blastp_wrapper", - "peptide_genomic_coordinate" + "pep_pointer" ], "update_time": "2021-03-19", "versions": 0 @@ -171614,13 +186946,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Visualisation", "Sequence contamination filtering", - "Statistical calculation", - "Taxonomic classification", "Sequence composition calculation", + "Visualisation", + "Statistical calculation", + "Validation", "Sequencing quality control", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "4c7e0703aace6aa3", @@ -171637,11 +186969,11 @@ ], "tools": [ "kraken2", - "porechop", - "tp_replace_in_line", - "taxonomy_krona_chart", "fastp", "multiqc", + "tp_replace_in_line", + "porechop", + "taxonomy_krona_chart", "Remove beginning1", "fastqc", "datamash_reverse" @@ -171668,12 +187000,12 @@ "galaxy-training-network" ], "tools": [ - "cardinal_data_exporter", - "cardinal_filtering", - "cardinal_quality_report", "cardinal_spectra_plots", "Filter1", - "cardinal_mz_images" + "cardinal_filtering", + "cardinal_quality_report", + "cardinal_mz_images", + "cardinal_data_exporter" ], "update_time": "2021-03-19", "versions": 0 @@ -171697,11 +187029,11 @@ "galaxy-training-network" ], "tools": [ + "Show beginning1", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "Show beginning1", - "gops_join_1" + "Grouping1" ], "update_time": "2021-03-19", "versions": 0 @@ -171711,16 +187043,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "Data handling", + "SNP detection" ], "edam_topic": [], "id": "51b745f8c964e5c6", @@ -171736,19 +187068,19 @@ "galaxy-training-network" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", + "samtools_stats", "snpSift_extractFields", "collapse_dataset", - "samtools_view", - "fasterq_dump", - "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "fastp", + "fasterq_dump", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-03-19", "versions": 0 @@ -171772,12 +187104,12 @@ "galaxy-training-network" ], "tools": [ - "get_flanks1", "CONVERTER_interval_to_bed_0", + "tp_tail_tool", + "gops_intersect_1", "Grouping1", "tp_replace_in_column", - "gops_intersect_1", - "tp_tail_tool" + "get_flanks1" ], "update_time": "2021-03-19", "versions": 0 @@ -171787,10 +187119,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Visualisation", "Image analysis", - "Image annotation" + "Visualisation", + "Image annotation", + "Data handling" ], "edam_topic": [], "id": "2a1e4de0dc77bbed", @@ -171806,14 +187138,14 @@ "galaxy-training-network" ], "tools": [ + "unzip", "ip_binary_to_labelimage", - "ip_count_objects", - "ip_overlay_segmentation", "ip_filter_standard", + "ip_histogram_equalization", "ip_convertimage", + "ip_count_objects", "ip_threshold", - "unzip", - "ip_histogram_equalization", + "ip_overlay_segmentation", "ip_imageinfo" ], "update_time": "2021-03-19", @@ -171824,17 +187156,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", "Peak calling", + "Statistical calculation", "Sequence alignment", + "Sequencing quality control", + "Sequence composition calculation", "Gene regulatory network analysis", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "2b0a986519532412", @@ -171850,18 +187182,18 @@ "galaxy-training-network" ], "tools": [ - "deeptools_plot_heatmap", + "deeptools_plot_correlation", + "macs2_callpeak", "deeptools_multi_bam_summary", - "bedtools_intersectbed", + "samtools_idxstats", "trimmomatic", - "deeptools_plot_fingerprint", - "bwa", - "deeptools_plot_correlation", "deeptools_bam_compare", - "fastqc", + "deeptools_plot_fingerprint", + "bedtools_intersectbed", + "deeptools_plot_heatmap", "deeptools_compute_matrix", - "macs2_callpeak", - "samtools_idxstats" + "fastqc", + "bwa" ], "update_time": "2021-03-19", "versions": 0 @@ -171887,16 +187219,16 @@ "galaxy-training-network" ], "tools": [ - "ambertools_acpype", - "gmx_editconf", - "get_pdb", "gmx_solvate", - "tp_grep_tool", - "gmx_sim", + "gmx_setup", "gmx_merge_topology_files", + "ambertools_acpype", + "get_pdb", "openbabel_compound_convert", "gmx_em", - "gmx_setup" + "gmx_editconf", + "tp_grep_tool", + "gmx_sim" ], "update_time": "2021-03-19", "versions": 0 @@ -171921,12 +187253,12 @@ ], "tools": [ "bio3d_pca_visualize", - "gmx_editconf", - "md_converter", "bio3d_pca", - "bio3d_rmsf", "vmd_hbonds", + "bio3d_rmsf", + "gmx_editconf", "bio3d_rmsd", + "md_converter", "mdanalysis_cosine_analysis" ], "update_time": "2021-03-19", @@ -171937,24 +187269,24 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence assembly", - "Read alignment", - "Box-Whisker plot plotting", - "Sequence assembly visualisation", + "Gene prediction", + "Genome annotation", "Genome assembly", + "Analysis", + "Sequence assembly visualisation", + "Sequence assembly", "Mapping assembly", - "Genome indexing", - "Generation", - "Cross-assembly", "Scatter plot plotting", - "Read mapping", "Sequence alignment", - "Genome visualisation", - "Gene prediction", - "Analysis", - "Genome annotation", - "Coding region prediction" + "Cross-assembly", + "Box-Whisker plot plotting", + "Coding region prediction", + "De-novo assembly", + "Generation", + "Genome indexing", + "Read alignment", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "b5403e4fff2961f9", @@ -171970,15 +187302,15 @@ "galaxy-training-network" ], "tools": [ - "bwa_mem", - "flye", - "bandage_image", - "nanoplot", - "fasta-stats", "pilon", - "jbrowse", + "bandage_info", + "flye", "prokka", - "bandage_info" + "fasta-stats", + "nanoplot", + "bandage_image", + "bwa_mem", + "jbrowse" ], "update_time": "2021-03-19", "versions": 0 @@ -171988,12 +187320,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Phylogenetic tree reconstruction", + "Phylogenetic tree generation", "Genome assembly", - "Phylogenetic tree analysis", "Sequence analysis", + "Phylogenetic tree analysis", "Phylogenetic analysis", - "Phylogenetic tree generation" + "Phylogenetic tree reconstruction" ], "edam_topic": [], "id": "3fd2195b6928d5e0", @@ -172007,8 +187339,8 @@ "tags": [], "tools": [ "roary", - "iqtree", - "newick_display" + "newick_display", + "iqtree" ], "update_time": "2021-03-11", "versions": 13 @@ -172018,16 +187350,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", "Statistical calculation", - "Genome indexing", + "Sequence alignment", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", "Generation", - "Validation" + "Genome indexing", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "3c1b1f210c7c292b", @@ -172040,12 +187372,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa", + "samtools_idxstats", "fastp", "multiqc", "picard_SortSam", "fastqc", - "samtools_idxstats" + "bwa" ], "update_time": "2021-03-10", "versions": 24 @@ -172098,19 +187430,19 @@ ], "tools": [ "cat1", - "collapse_dataset", - "Cut1", - "samtools_view", "param_value_from_file", "createInterval", "__MERGE_COLLECTION__", - "tp_text_file_with_recurring_lines", - "__RELABEL_FROM_FILE__", "tp_head_tool", - "split_file_to_collection", + "collapse_dataset", + "bedtools_intersectbed", "__BUILD_LIST__", + "split_file_to_collection", + "tp_text_file_with_recurring_lines", "tp_replace_in_column", - "bedtools_intersectbed" + "Cut1", + "__RELABEL_FROM_FILE__", + "samtools_view" ], "update_time": "2021-03-03", "versions": 1 @@ -172138,12 +187470,12 @@ "covid19.galaxyproject.org" ], "tools": [ - "deeptools_bam_coverage", - "filter_by_fasta_ids", "picard_NormalizeFasta", "samtools_fastx", - "samtools_view", - "minimap2" + "deeptools_bam_coverage", + "filter_by_fasta_ids", + "minimap2", + "samtools_view" ], "update_time": "2021-03-03", "versions": 2 @@ -172169,20 +187501,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "bedtools_genomecoveragebed", + "bcftools_consensus", + "Filter1", "Add_a_column1", - "gops_concat_1", "gops_subtract_1", + "gops_concat_1", "collapse_dataset", - "bedtools_maskfastabed", - "Cut1", "tp_find_and_replace", - "bcftools_consensus", - "gops_merge_1", "compose_text_param", - "Filter1", + "Cut1", "vcf2tsv", - "snpSift_filter" + "gops_merge_1", + "bedtools_maskfastabed", + "snpSift_filter", + "bedtools_genomecoveragebed" ], "update_time": "2021-03-03", "versions": 1 @@ -172192,15 +187524,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "76bb6bde19975e05", @@ -172219,22 +187551,22 @@ "fastq->vcf" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", + "__FILTER_FROM_FILE__", + "samtools_stats", + "Filter1", "collapse_dataset", + "lofreq_viterbi", "snpeff_sars_cov_2", "Cut1", - "samtools_view", - "__FILTER_FROM_FILE__", - "tp_grep_tool", - "samtools_stats", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "Filter1" + "lofreq_filter", + "lofreq_indelqual", + "bwa_mem", + "lofreq_call", + "tp_grep_tool", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-03-03", "versions": 1 @@ -172244,15 +187576,15 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "0c6f7bfc826433c4", @@ -172270,20 +187602,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-03-03", "versions": 1 @@ -172293,14 +187625,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "7fd58f5fc93f414e", @@ -172317,22 +187649,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-03-03", "versions": 1 @@ -172342,15 +187674,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bd1cf22d47389742", @@ -172366,17 +187698,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-03-03", "versions": 1 @@ -172387,11 +187719,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "31dbd313e5c8160b", @@ -172407,15 +187739,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-03-03", "versions": 1 @@ -172439,20 +187771,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", + "Filter1", "Add_a_column1", - "tp_sort_header_tool", - "collapse_dataset", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", "split_file_to_collection", - "Filter1", - "snpSift_filter" + "tp_sort_header_tool", + "tp_easyjoin_tool", + "snpSift_filter", + "replace_column_with_key_value_file", + "datamash_ops" ], "update_time": "2021-03-03", "versions": 1 @@ -172476,23 +187808,23 @@ "covid19.galaxyproject.org" ], "tools": [ - "tp_easyjoin_tool", - "tp_split_on_column", - "Add_a_column1", "cat1", - "tp_sort_header_tool", - "collapse_dataset", + "Filter1", + "Add_a_column1", "snpSift_extractFields", - "Cut1", + "snpfreqplot", + "collapse_dataset", "tp_find_and_replace", - "datamash_ops", "compose_text_param", - "replace_column_with_key_value_file", - "snpfreqplot", + "Cut1", + "tp_tail_tool", "tp_head_tool", - "Filter1", + "tp_sort_header_tool", + "tp_easyjoin_tool", "snpSift_filter", - "tp_tail_tool" + "replace_column_with_key_value_file", + "datamash_ops", + "tp_split_on_column" ], "update_time": "2021-02-22", "versions": 1 @@ -172503,11 +187835,11 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", + "Validation", "Sequencing quality control", "Read mapping", - "SNP detection", "Formatting", - "Validation" + "SNP detection" ], "edam_topic": [], "id": "a29670ff0ecb1a38", @@ -172523,15 +187855,15 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "picard_MarkDuplicates", + "bowtie2", + "lofreq_viterbi", "snpeff_sars_cov_2", + "lofreq_filter", "fastp", - "lofreq_viterbi", - "lofreq_call", - "lofreq_indelqual", "multiqc", - "bowtie2" + "lofreq_indelqual", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2021-02-22", "versions": 1 @@ -172541,14 +187873,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "e439a0e17a90d24c", @@ -172565,22 +187897,22 @@ "covid19.galaxyproject.org" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "fastp", - "lofreq_viterbi", - "lofreq_call", "lofreq_indelqual", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-02-22", "versions": 1 @@ -172590,15 +187922,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "fedf2874752ac1f6", @@ -172614,17 +187946,17 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "samtools_view", "samtools_stats", - "fastp", "lofreq_viterbi", - "lofreq_call", + "snpeff_sars_cov_2", + "lofreq_filter", + "fastp", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "samtools_view", + "picard_MarkDuplicates" ], "update_time": "2021-02-22", "versions": 1 @@ -172634,15 +187966,15 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Sequence assembly", "Sequencing quality control", + "Base-calling", "Pairwise sequence alignment", "Variant calling", - "Statistical calculation", - "Sequence contamination filtering", - "SNP detection", "Validation", - "Base-calling" + "SNP detection" ], "edam_topic": [], "id": "47ce6a2d30887637", @@ -172660,20 +187992,20 @@ "covid19.galaxyproject.org" ], "tools": [ - "lofreq_filter", - "bamleftalign", - "snpeff_sars_cov_2", - "medaka_consensus", + "samtools_stats", "medaka_variant", - "samtools_view", "tp_find_and_replace", - "minimap2", - "samtools_stats", + "snpeff_sars_cov_2", + "lofreq_filter", "fastp", "multiqc", - "qualimap_bamqc", + "medaka_consensus", "__FLATTEN__", - "ivar_trim" + "ivar_trim", + "minimap2", + "bamleftalign", + "samtools_view", + "qualimap_bamqc" ], "update_time": "2021-02-22", "versions": 1 @@ -172683,9 +188015,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -172699,9 +188031,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", + "ivar_consensus", "samtools_slice_bam", - "ivar_consensus" + "bwa_mem" ], "update_time": "2021-02-14", "versions": 2 @@ -172711,9 +188043,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -172727,9 +188059,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", + "ivar_consensus", "samtools_slice_bam", - "ivar_consensus" + "bwa_mem" ], "update_time": "2021-02-14", "versions": 7 @@ -172739,9 +188071,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -172755,9 +188087,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", + "ivar_consensus", "samtools_slice_bam", - "ivar_consensus" + "bwa_mem" ], "update_time": "2021-02-14", "versions": 10 @@ -172767,21 +188099,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Mapping assembly", - "De-novo assembly", + "Genome assembly", + "Analysis", + "Sequence assembly visualisation", "Sequence assembly", - "Read mapping", - "Read alignment", + "Mapping assembly", + "Scatter plot plotting", "Sequence alignment", + "Cross-assembly", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Genome visualisation", - "Analysis", - "Genome assembly", - "Genome indexing", + "De-novo assembly", "Generation", - "Cross-assembly" + "Genome indexing", + "Read alignment", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "22bd45f60c60a338", @@ -172796,14 +188128,14 @@ "assembly" ], "tools": [ - "bwa_mem", + "pilon", + "bandage_info", "flye", - "bandage_image", - "nanoplot", "fasta-stats", - "pilon", - "jbrowse", - "bandage_info" + "nanoplot", + "bandage_image", + "bwa_mem", + "jbrowse" ], "update_time": "2020-12-08", "versions": 4 @@ -172813,20 +188145,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Scatter plot plotting", - "Mapping assembly", - "De-novo assembly", + "Genome assembly", + "Analysis", + "Sequence assembly visualisation", "Sequence assembly", - "Read mapping", - "Read alignment", + "Mapping assembly", + "Scatter plot plotting", "Sequence alignment", + "Cross-assembly", "Box-Whisker plot plotting", - "Sequence assembly visualisation", - "Analysis", - "Genome assembly", - "Genome indexing", + "De-novo assembly", "Generation", - "Cross-assembly" + "Genome indexing", + "Read alignment", + "Read mapping" ], "edam_topic": [], "id": "2cb16d321a804b1a", @@ -172841,13 +188173,13 @@ "assembly" ], "tools": [ - "bwa_mem", + "pilon", + "bandage_info", "flye", - "bandage_image", - "nanoplot", "fasta-stats", - "pilon", - "bandage_info" + "nanoplot", + "bandage_image", + "bwa_mem" ], "update_time": "2020-12-08", "versions": 10 @@ -172882,11 +188214,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "59d6ee23bff41eec", @@ -172901,8 +188233,8 @@ "assembly" ], "tools": [ - "bwa_mem", - "jbrowse" + "jbrowse", + "bwa_mem" ], "update_time": "2020-12-08", "versions": 2 @@ -172912,11 +188244,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", + "Statistical calculation", "Gene expression analysis", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Sequencing quality control" ], "edam_topic": [], "id": "b0614274c66efa95", @@ -172929,9 +188261,9 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "collapse_dataset", "salmon", - "fastqc", - "collapse_dataset" + "fastqc" ], "update_time": "2020-10-19", "versions": 4 @@ -172956,8 +188288,8 @@ ], "tools": [ "Grep1", - "cardinal_quality_report", "tp_sort_header_tool", + "cardinal_quality_report", "cardinal_data_exporter" ], "update_time": "2020-08-31", @@ -172968,14 +188300,14 @@ "creators": [], "doi": "", "edam_operation": [ + "Visualisation", + "Statistical calculation", "Clustering", - "Heat map generation", + "Standardisation and normalisation", + "Principal component plotting", "Protein quantification", "Imputation", - "Standardisation and normalisation", - "Visualisation", - "Statistical calculation", - "Principal component plotting" + "Heat map generation" ], "edam_topic": [], "id": "43a951ec514498f6", @@ -172992,9 +188324,9 @@ ], "tools": [ "Add_a_column1", + "histogram_rpy", "tp_sort_header_tool", "Cut1", - "histogram_rpy", "maxquant" ], "update_time": "2020-08-31", @@ -173019,19 +188351,19 @@ "galaxy-training-network" ], "tools": [ - "MSGFPlusAdapter", - "IDFilter", + "FileMerger", "FeatureFinderMultiplex", "FalseDiscoveryRate", - "IDConflictResolver", - "MzTabExporter", "PeptideIndexer", + "HighResPrecursorMassCorrector", + "IDFilter", + "IDConflictResolver", "ConsensusID", "IDMapper", - "FileMerger", + "MSGFPlusAdapter", + "IDMerger", "FileFilter", - "HighResPrecursorMassCorrector", - "IDMerger" + "MzTabExporter" ], "update_time": "2020-08-31", "versions": 0 @@ -173056,10 +188388,10 @@ ], "tools": [ "FileConverter", - "peptide_shaker", - "search_gui", + "PeakPickerHiRes", "Grep1", - "PeakPickerHiRes" + "search_gui", + "peptide_shaker" ], "update_time": "2020-08-31", "versions": 0 @@ -173084,10 +188416,10 @@ ], "tools": [ "FileConverter", - "peptide_shaker", - "search_gui", + "PeakPickerHiRes", "Grep1", - "PeakPickerHiRes" + "search_gui", + "peptide_shaker" ], "update_time": "2020-08-31", "versions": 0 @@ -173111,17 +188443,17 @@ "galaxy-training-network" ], "tools": [ - "MSGFPlusAdapter", - "IDScoreSwitcher", - "IDFilter", "FalseDiscoveryRate", - "FidoAdapter", + "IDPosteriorErrorProbability", "PeptideIndexer", "FileInfo", + "IDFilter", + "FidoAdapter", "ConsensusID", - "IDPosteriorErrorProbability", + "MSGFPlusAdapter", + "IDMerger", "XTandemAdapter", - "IDMerger" + "IDScoreSwitcher" ], "update_time": "2020-08-31", "versions": 0 @@ -173145,16 +188477,16 @@ "galaxy-training-network" ], "tools": [ - "IDScoreSwitcher", - "XTandemAdapter", - "IDFilter", "FalseDiscoveryRate", - "FidoAdapter", + "IDPosteriorErrorProbability", "PeptideIndexer", + "Grep1", + "IDFilter", + "FidoAdapter", "TextExporter", "FileInfo", - "IDPosteriorErrorProbability", - "Grep1" + "XTandemAdapter", + "IDScoreSwitcher" ], "update_time": "2020-08-31", "versions": 0 @@ -173181,14 +188513,14 @@ "galaxy-training-network" ], "tools": [ + "sklearn_searchcv", + "sklearn_generalized_linear", "sklearn_build_pipeline", - "sklearn_svm_classifier", "sklearn_ensemble", - "sklearn_generalized_linear", + "plotly_ml_performance_plots", "sklearn_nn_classifier", + "sklearn_svm_classifier", "Remove beginning1", - "sklearn_searchcv", - "plotly_ml_performance_plots", "sklearn_estimator_attributes" ], "update_time": "2020-08-31", @@ -173217,9 +188549,9 @@ "galaxy-training-network" ], "tools": [ + "ggplot2_point", "sklearn_numeric_clustering", - "csv_to_tabular", - "ggplot2_point" + "csv_to_tabular" ], "update_time": "2020-08-31", "versions": 0 @@ -173229,16 +188561,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Statistical calculation", + "Phylogenetic tree generation", "Sequencing quality control", + "Sequence composition calculation", "Variant calling", - "Phylogenetic tree generation", + "Validation", + "Phylogenetic tree visualisation", "Genome visualisation", "Antimicrobial resistance prediction", - "Statistical calculation", - "Taxonomic classification", - "Phylogenetic tree visualisation", - "Validation" + "Taxonomic classification" ], "edam_topic": [], "id": "5693811cd933d2a2", @@ -173255,15 +188587,15 @@ "galaxy-training-network" ], "tools": [ - "tb_profiler_profile", - "tbvcfreport", "kraken2", "trimmomatic", + "multiqc", "tb_variant_filter", + "tbvcfreport", + "fastqc", "snippy", - "multiqc", "jbrowse", - "fastqc" + "tb_profiler_profile" ], "update_time": "2020-08-31", "versions": 0 @@ -173273,16 +188605,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read mapping", - "Generation", + "Sequence contamination filtering", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", - "Sequence contamination filtering", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "Data handling", + "SNP detection" ], "edam_topic": [], "id": "30a601039d24e2eb", @@ -173298,17 +188630,17 @@ "galaxy-training-network" ], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "snpeff_sars_cov_2", - "snpSift_extractFields", - "fasterq_dump", "samtools_stats", + "snpSift_extractFields", "lofreq_viterbi", + "snpeff_sars_cov_2", "fastp", - "lofreq_call", + "fasterq_dump", + "multiqc", "lofreq_indelqual", - "multiqc" + "bwa_mem", + "lofreq_call", + "picard_MarkDuplicates" ], "update_time": "2020-08-31", "versions": 0 @@ -173344,17 +188676,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Mapping", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", "Peak calling", - "Gene regulatory network analysis", + "Statistical calculation", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", + "Gene regulatory network analysis", "Read pre-processing", "Sequence trimming", - "Statistical calculation" + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "daff6854b5dfc6f1", @@ -173370,27 +188702,27 @@ "galaxy-training-network" ], "tools": [ - "deeptools_multi_bam_summary", + "deeptools_plot_correlation", "gops_concat_1", - "trim_galore", + "deeptools_bam_coverage", + "deeptools_bam_compare", "fastqc", + "bowtie2", + "Filter1", + "Add_a_column1", + "deeptools_multi_bam_summary", "samtools_idxstats", + "deeptools_plot_heatmap", + "tp_sort_header_tool", "deeptools_compute_matrix", - "deeptools_plot_correlation", - "datamash_ops", "macs2_callpeak", - "Add_a_column1", - "tp_sort_header_tool", - "deeptools_bam_compare", - "deeptools_bam_coverage", "cat1", - "deeptools_plot_heatmap", "deeptools_plot_fingerprint", + "bedtools_mergebed", + "trim_galore", "bedtools_sortbed", - "Filter1", - "bowtie2", "bedtools_intersectbed", - "bedtools_mergebed" + "datamash_ops" ], "update_time": "2020-08-31", "versions": 0 @@ -173400,9 +188732,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "91c8daa5f2bcf7c0", @@ -173418,15 +188750,15 @@ "galaxy-training-network" ], "tools": [ - "metilene", + "bwameth", + "tp_tail_tool", + "deeptools_compute_matrix", "deeptools_plot_profile", + "fastqc", "pileometh", - "tp_awk_tool", - "bwameth", "replace_column_with_key_value_file", - "fastqc", - "deeptools_compute_matrix", - "tp_tail_tool" + "metilene", + "tp_awk_tool" ], "update_time": "2020-08-31", "versions": 0 @@ -173436,21 +188768,21 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Enrichment analysis", - "Sequencing quality control", - "Formatting", "Peak calling", - "Visualisation", - "Gene regulatory network analysis", "Statistical calculation", + "Visualisation", "Primer removal", + "Sequencing quality control", + "Formatting", + "Sequence composition calculation", + "Gene regulatory network analysis", + "Sequence alignment analysis", "Read pre-processing", - "Mapping", - "Sequence trimming" + "Data handling", + "Sequence trimming", + "Read mapping", + "Enrichment analysis", + "Mapping" ], "edam_topic": [], "id": "99821674db7682bb", @@ -173466,22 +188798,22 @@ "galaxy-training-network" ], "tools": [ - "picard_CollectInsertSizeMetrics", - "deeptools_plot_heatmap", "bowtie2", - "picard_MarkDuplicates", - "bedtools_bamtobed", - "tp_awk_tool", - "pygenomeTracks", - "samtools_sort", + "macs2_callpeak", + "picard_CollectInsertSizeMetrics", "wig_to_bigWig", - "bedtools_sortbed", + "samtools_sort", + "deeptools_plot_heatmap", "genrich", - "fastqc", + "bedtools_sortbed", "deeptools_compute_matrix", - "macs2_callpeak", + "bedtools_bamtobed", + "fastqc", "bamFilter", - "cutadapt" + "cutadapt", + "pygenomeTracks", + "tp_awk_tool", + "picard_MarkDuplicates" ], "update_time": "2020-08-31", "versions": 0 @@ -173492,9 +188824,9 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", "Phylogenetic tree generation", - "Genome visualisation" + "Genome visualisation", + "Variant calling" ], "edam_topic": [], "id": "1719e0eb54b41f68", @@ -173521,10 +188853,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Genetic variation analysis", + "Statistical calculation", "Sequence analysis", - "Variant calling", - "Statistical calculation" + "Genetic variation analysis", + "Variant calling" ], "edam_topic": [], "id": "ac89c2d51c32cc9c", @@ -173540,13 +188872,13 @@ "galaxy-training-network" ], "tools": [ - "gemini_db_info", - "snpEff_download", - "gemini_load", - "gemini_query", "snpEff", "freebayes", - "vcfallelicprimitives" + "gemini_load", + "snpEff_download", + "vcfallelicprimitives", + "gemini_query", + "gemini_db_info" ], "update_time": "2020-08-31", "versions": 0 @@ -173570,14 +188902,14 @@ "galaxy-training-network" ], "tools": [ - "mimodd_varreport", + "snpEff", "snpEff_download", - "mimodd_varextract", "tp_find_and_replace", + "mimodd_varreport", + "mimodd_varextract", + "mimodd_varcall", "mimodd_vcf_filter", - "snpEff", - "mimodd_map", - "mimodd_varcall" + "mimodd_map" ], "update_time": "2020-08-31", "versions": 0 @@ -173587,17 +188919,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "2362ff8880213586", @@ -173613,16 +188945,16 @@ "galaxy-training-network" ], "tools": [ - "bwa_mem", - "bamleftalign", - "picard_MarkDuplicates", + "freebayes", "picard_MergeSamFiles", "vcffilter2", - "Cut1", - "freebayes", + "vcf2tsv", + "bwa_mem", "fastqc", "bamFilter", - "vcf2tsv" + "Cut1", + "bamleftalign", + "picard_MarkDuplicates" ], "update_time": "2020-08-31", "versions": 0 @@ -173632,17 +188964,17 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Variant calling", - "Sequence alignment", - "Genetic variation analysis", - "Sequence analysis", "Statistical calculation", - "Genome indexing", + "Genetic variation analysis", + "Sequence alignment", + "Sequencing quality control", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Sequence analysis", + "Variant calling", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "5442f0437ade82c4", @@ -173658,15 +188990,15 @@ "galaxy-training-network" ], "tools": [ - "bcftools_norm", - "bwa_mem", - "gemini_load", "samtools_rmdup", - "snpEff", - "freebayes", "samtool_filter2", + "freebayes", + "bcftools_norm", + "snpEff", + "gemini_load", "multiqc", "gemini_inheritance", + "bwa_mem", "fastqc" ], "update_time": "2020-08-31", @@ -173677,10 +189009,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Genetic variation analysis", + "Statistical calculation", "Sequence analysis", - "Variant calling", - "Statistical calculation" + "Genetic variation analysis", + "Variant calling" ], "edam_topic": [], "id": "1be22b394f9ec3ab", @@ -173696,12 +189028,12 @@ "galaxy-training-network" ], "tools": [ - "bcftools_norm", - "gemini_load", - "samtools_rmdup", - "snpEff", "freebayes", + "snpEff", + "samtools_rmdup", "samtool_filter2", + "bcftools_norm", + "gemini_load", "gemini_inheritance" ], "update_time": "2020-08-31", @@ -173723,11 +189055,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "tp_head_tool", + "gops_join_1", "tp_sort_header_tool", "comp1", - "Grouping1", - "tp_head_tool", - "gops_join_1" + "Grouping1" ], "update_time": "2020-08-10", "versions": 0 @@ -173737,14 +189069,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Generation", - "Sequencing quality control", - "Sequence alignment", "Sequence contamination filtering", + "Sequence alignment", + "Sequencing quality control", + "Generation", "Genome indexing", - "SNP detection", - "Validation" + "Validation", + "Read mapping", + "SNP detection" ], "edam_topic": [], "id": "bcf230e526632064", @@ -173760,24 +189092,24 @@ "artic" ], "tools": [ + "samtools_stats", + "lofreq_viterbi", + "snpeff_sars_cov_2", "lofreq_filter", - "__ZIP_COLLECTION__", - "bwa_mem", + "fastp", + "multiqc", "vcfvcfintersect", - "snpeff_sars_cov_2", - "samtools_view", "tp_replace_in_line", - "samtools_stats", - "__UNZIP_COLLECTION__", - "fastp", - "lofreq_viterbi", + "__ZIP_COLLECTION__", "lofreq_indelqual", - "lofreq_call", - "multiqc", - "qualimap_bamqc", - "__FLATTEN__", "ivar_removereads", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "__FLATTEN__", + "lofreq_call", + "samtools_view", + "__UNZIP_COLLECTION__", + "qualimap_bamqc" ], "update_time": "2020-06-28", "versions": 3 @@ -173787,13 +189119,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequence annotation", - "RNA-Seq analysis", - "Sequencing quality control", + "Statistical calculation", + "Transcriptome assembly", "Sequence alignment", - "Transcriptome assembly" + "Sequencing quality control", + "Sequence annotation", + "RNA-Seq analysis" ], "edam_topic": [], "id": "e045a6064ad5fdc4", @@ -173806,14 +189138,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "deeptools_bam_coverage", - "gffcompare", - "fastq_groomer", + "CONVERTER_gz_to_uncompressed", "trimmomatic", - "hisat2", + "deeptools_bam_coverage", "fastqc", + "gffcompare", "stringtie", - "CONVERTER_gz_to_uncompressed" + "hisat2", + "fastq_groomer" ], "update_time": "2020-06-25", "versions": 6 @@ -173823,14 +189155,14 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Sequencing quality control", - "Formatting", - "Sequence alignment", "Sequence contamination filtering", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence alignment", + "Validation", + "Sequencing quality control", + "Read mapping", + "Formatting" ], "edam_topic": [], "id": "ccf936c5b2f2c2f3", @@ -173843,16 +189175,16 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", - "picard_MarkDuplicates", - "tp_sed_tool", "samtool_filter2", - "fastp", + "qualimap_bamqc", "ivar_consensus", "multiqc", - "qualimap_bamqc", + "fastp", "ivar_variants", - "ivar_trim" + "tp_sed_tool", + "bwa_mem", + "ivar_trim", + "picard_MarkDuplicates" ], "update_time": "2020-06-20", "versions": 14 @@ -173862,18 +189194,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence alignment analysis", - "Sequence composition calculation", - "Read mapping", - "Sequencing quality control", - "Formatting", - "Variant calling", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", + "Sequencing quality control", "Sequence file editing", + "Formatting", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Sequence alignment analysis", + "Variant calling", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "1a159863e9d977a0", @@ -173886,22 +189218,22 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", - "sam_merge2", - "picard_MarkDuplicates", - "tp_sort_header_tool", - "vcffilter2", - "snpSift_extractFields", - "snpEff", + "seqtk_trimfq", "freebayes", + "snpEff", + "picard_CleanSam", + "snpSift_extractFields", + "sam_merge2", + "picard_AddOrReplaceReadGroups", "vcfallelicprimitives", + "vcffilter2", + "tp_sort_header_tool", "Remove beginning1", - "seqtk_trimfq", "Grouping1", + "bwa_mem", "fastqc", "bamFilter", - "picard_CleanSam", - "picard_AddOrReplaceReadGroups" + "picard_MarkDuplicates" ], "update_time": "2020-06-19", "versions": 5 @@ -173912,12 +189244,12 @@ "doi": "", "edam_operation": [ "Sequence contamination filtering", - "Read mapping", - "Genome indexing", "Generation", - "Sequencing quality control", + "Genome indexing", "Sequence alignment", - "Validation" + "Validation", + "Sequencing quality control", + "Read mapping" ], "edam_topic": [], "id": "fca05a51c9c91df4", @@ -173933,13 +189265,13 @@ "artic" ], "tools": [ - "bwa_mem", - "fastp", "ivar_consensus", "multiqc", - "qualimap_bamqc", + "fastp", "ivar_variants", - "ivar_trim" + "bwa_mem", + "ivar_trim", + "qualimap_bamqc" ], "update_time": "2020-05-25", "versions": 2 @@ -173962,15 +189294,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cut_fr", - "bg_column_arrange_by_header", - "Cut1", + "Paste1", "regex1", - "biom_convert", - "row_means", + "cut_fr", "Remove beginning1", "krona-text", - "Paste1" + "bg_column_arrange_by_header", + "row_means", + "Cut1", + "biom_convert" ], "update_time": "2020-05-19", "versions": 1 @@ -173980,9 +189312,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "80a1493fb9593bb3", @@ -173995,13 +189327,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cummeRbund", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-18", @@ -174012,10 +189344,10 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Sequencing quality control", - "Validation" + "Statistical calculation", + "Validation", + "Sequencing quality control" ], "edam_topic": [], "id": "d3989c6c2c663cd3", @@ -174028,13 +189360,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", + "cufflinks", "fastq_quality_trimmer", - "cuffdiff", "tophat2", "multiqc", - "cufflinks", "fastqc", + "cummeRbund", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-15", @@ -174045,9 +189377,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "115896e8f4059e44", @@ -174060,12 +189392,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-15", @@ -174076,9 +189408,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "73854e391eec51d0", @@ -174091,10 +189423,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastqc", "cuffdiff", + "trimmomatic", "tophat2", - "trimmomatic" + "fastqc" ], "update_time": "2020-05-15", "versions": 9 @@ -174127,9 +189459,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "1ac197bae296b2bf", @@ -174142,14 +189474,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", - "fastq_groomer", - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", - "cuffmerge" + "tophat2", + "fastqc", + "cummeRbund", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2020-05-14", "versions": 2 @@ -174159,9 +189491,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "189c584ea4bde59a", @@ -174174,14 +189506,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", - "fastq_groomer", - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", - "cuffmerge" + "tophat2", + "fastqc", + "cummeRbund", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2020-05-14", "versions": 2 @@ -174191,9 +189523,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d68e167c3423c795", @@ -174206,12 +189538,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174222,9 +189554,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "9176f8ebac92d10c", @@ -174237,11 +189569,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", "fastq_quality_trimmer", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174252,9 +189584,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "581c455f74aa55a4", @@ -174267,14 +189599,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", - "fastq_groomer", - "cuffdiff", - "tophat2", "cufflinks", - "fastqc", "Filter1", - "cuffmerge" + "tophat2", + "fastqc", + "cummeRbund", + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2020-05-14", "versions": 0 @@ -174284,9 +189616,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "427e27f87b8048a3", @@ -174299,13 +189631,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", + "cufflinks", "fastq_quality_trimmer", - "cuffdiff", + "Filter1", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cummeRbund", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174316,9 +189648,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "52d2fb868defa474", @@ -174331,13 +189663,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", "tabular_to_csv", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174348,11 +189680,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Primer removal", "Read pre-processing", - "Sequence trimming", - "Statistical calculation", "Sequence composition calculation", + "Statistical calculation", + "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -174366,11 +189698,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "trim_galore", - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", + "trim_galore", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174381,9 +189713,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "0427bd5f28789a1f", @@ -174396,12 +189728,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174412,11 +189744,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -174430,11 +189762,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", "fastqc", "cutadapt", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174445,9 +189777,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "84589f66ec87ad99", @@ -174460,12 +189792,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174476,11 +189808,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -174494,11 +189826,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", "fastqc", "cutadapt", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174509,11 +189841,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Statistical calculation", "Sequence composition calculation", - "Primer removal", + "Statistical calculation", "Read pre-processing", "Sequence trimming", + "Primer removal", "Sequencing quality control" ], "edam_topic": [], @@ -174527,11 +189859,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", "cufflinks", + "tophat2", "fastqc", "cutadapt", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-14", @@ -174542,9 +189874,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "cc6de673126c56cb", @@ -174557,14 +189889,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cummeRbund", + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", "tabular_to_csv", - "cufflinks", "fastqc", - "Filter1", + "cummeRbund", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-13", @@ -174575,9 +189907,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "50fdbdb8f807c021", @@ -174590,11 +189922,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2020-05-13", @@ -174605,12 +189937,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Read summarisation", "Sequence alignment analysis", - "Sequencing quality control", "Sequence alignment", - "RNA-Seq quantification" + "RNA-Seq quantification", + "Read summarisation", + "Sequencing quality control", + "Data handling" ], "edam_topic": [], "id": "7ae06a27188b9438", @@ -174626,11 +189958,11 @@ "galaxy-training-network" ], "tools": [ - "rna_star", "featurecounts", - "umi_tools_count", + "bamFilter", "umi_tools_extract", - "bamFilter" + "rna_star", + "umi_tools_count" ], "update_time": "2020-04-22", "versions": 0 @@ -174640,8 +189972,8 @@ "creators": [], "doi": "", "edam_operation": [ - "Expression profile clustering", "Expression analysis", + "Expression profile clustering", "Molecular dynamics" ], "edam_topic": [], @@ -174658,11 +189990,11 @@ "galaxy-training-network" ], "tools": [ - "raceid_filtnormconf", - "raceid_trajectory", + "raceid_inspectclusters", "raceid_clustering", + "raceid_filtnormconf", "raceid_inspecttrajectory", - "raceid_inspectclusters" + "raceid_trajectory" ], "update_time": "2020-04-22", "versions": 0 @@ -174673,8 +190005,8 @@ "doi": "", "edam_operation": [ "Read pre-processing", - "Sequence visualisation", - "Sequencing quality control" + "Sequencing quality control", + "Sequence visualisation" ], "edam_topic": [], "id": "3c9140288202aa76", @@ -174690,10 +190022,10 @@ "galaxy-training-network" ], "tools": [ - "scater_create_qcmetric_ready_sce", - "scater_plot_pca", "scater_plot_dist_scatter", - "scater_filter" + "scater_plot_pca", + "scater_filter", + "scater_create_qcmetric_ready_sce" ], "update_time": "2020-04-22", "versions": 0 @@ -174719,21 +190051,21 @@ "galaxy-training-network" ], "tools": [ - "anndata_inspect", - "anndata_manipulate", + "Filter1", "anndata_import", "scanpy_plot", - "tp_awk_tool", + "tp_tail_tool", "Cut1", - "scanpy_filter", + "anndata_manipulate", "scanpy_inspect", - "scanpy_normalize", - "scanpy_cluster_reduce_dimension", "tp_cat", + "scanpy_normalize", "scanpy_remove_confounders", - "Filter1", "tp_replace_in_column", - "tp_tail_tool" + "scanpy_cluster_reduce_dimension", + "scanpy_filter", + "anndata_inspect", + "tp_awk_tool" ], "update_time": "2020-04-22", "versions": 0 @@ -174759,12 +190091,12 @@ "galaxy-training-network" ], "tools": [ + "sklearn_searchcv", + "plotly_regression_performance_plots", + "sklearn_generalized_linear", "sklearn_build_pipeline", "sklearn_ensemble", - "sklearn_generalized_linear", - "Remove beginning1", - "sklearn_searchcv", - "plotly_regression_performance_plots" + "Remove beginning1" ], "update_time": "2020-04-09", "versions": 0 @@ -174789,8 +190121,8 @@ "galaxy-training-network" ], "tools": [ - "sklearn_ensemble", - "plotly_regression_performance_plots" + "plotly_regression_performance_plots", + "sklearn_ensemble" ], "update_time": "2020-04-09", "versions": 0 @@ -174866,8 +190198,8 @@ ], "tools": [ "plotly_parallel_coordinates_plot", - "sklearn_build_pipeline", - "sklearn_searchcv" + "sklearn_searchcv", + "sklearn_build_pipeline" ], "update_time": "2020-04-09", "versions": 0 @@ -174891,10 +190223,10 @@ "galaxy-training-network" ], "tools": [ - "sklearn_build_pipeline", "sklearn_searchcv", - "sklearn_ensemble", - "plotly_regression_performance_plots" + "plotly_regression_performance_plots", + "sklearn_build_pipeline", + "sklearn_ensemble" ], "update_time": "2020-04-09", "versions": 0 @@ -174905,8 +190237,8 @@ "doi": "", "edam_operation": [ "Optimisation and refinement", - "Sequence assembly", - "Genome assembly" + "Genome assembly", + "Sequence assembly" ], "edam_topic": [], "id": "8abcfe166f1a6cd8", @@ -174922,8 +190254,8 @@ "galaxy-training-network" ], "tools": [ - "spades", "fasta-stats", + "spades", "velvetoptimiser" ], "update_time": "2020-04-07", @@ -174934,13 +190266,13 @@ "creators": [], "doi": "", "edam_operation": [ - "De-novo assembly", - "Sequence composition calculation", + "Visualisation", + "Statistical calculation", "Sequencing quality control", "Formatting", + "De-novo assembly", + "Sequence composition calculation", "Sequence assembly validation", - "Visualisation", - "Statistical calculation", "Validation" ], "edam_topic": [], @@ -174957,11 +190289,11 @@ "galaxy-training-network" ], "tools": [ + "multiqc", + "velvetg", + "fastq_paired_end_interlacer", "velveth", "quast", - "fastq_paired_end_interlacer", - "velvetg", - "multiqc", "fastqc" ], "update_time": "2020-04-07", @@ -174972,9 +190304,9 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence alignment", "Read mapping", - "Mapping", - "Sequence alignment" + "Mapping" ], "edam_topic": [], "id": "b808cd1c0090b068", @@ -174990,26 +190322,26 @@ "galaxy-training-network" ], "tools": [ - "lastz_wrapper_2", - "tp_grep_tool", - "fasta_filter_by_length", - "tp_sed_tool", - "datamash_ops", - "mergeCols1", - "tp_sort_header_tool", - "bedtools_complementbed", "collapse_dataset", + "Cut1", + "tp_cat", + "Grep1", + "random_lines1", "join1", + "tp_grep_tool", + "Filter1", + "bedtools_complementbed", + "tp_sort_header_tool", "addValue", - "random_lines1", "fasta_compute_length", "cat1", - "Cut1", + "lastz_wrapper_2", "bedtools_sortbed", - "Filter1", - "Grep1", + "fasta_filter_by_length", + "mergeCols1", "bedtools_intersectbed", - "tp_cat" + "tp_sed_tool", + "datamash_ops" ], "update_time": "2020-04-07", "versions": 1 @@ -175019,16 +190351,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Aggregation", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", "Statistical calculation", + "Visualisation", "Genome assembly", + "Sequencing quality control", + "Aggregation", "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation", "Validation" ], "edam_topic": [], @@ -175045,10 +190377,10 @@ "galaxy-training-network" ], "tools": [ - "quast", - "multiqc", "prokka", "fastqc", + "multiqc", + "quast", "unicycler" ], "update_time": "2020-04-07", @@ -175073,11 +190405,11 @@ "galaxy-training-network" ], "tools": [ - "get_pdb", "gmx_solvate", - "gmx_sim", + "gmx_setup", + "get_pdb", "gmx_em", - "gmx_setup" + "gmx_sim" ], "update_time": "2020-04-07", "versions": 1 @@ -175113,19 +190445,19 @@ "creators": [], "doi": "", "edam_operation": [ + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", - "Pairwise sequence alignment", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", + "Pairwise sequence alignment", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping" ], "edam_topic": [], "id": "557601292ea0f6f3", @@ -175141,15 +190473,15 @@ "alternate-pre-processing" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "minimap2", "samtool_filter2", - "fastp", + "samtools_fastx", + "picard_MergeSamFiles", "multiqc", - "fastqc" + "fastp", + "nanoplot", + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-02-23", "versions": 2 @@ -175159,15 +190491,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Statistical calculation", "Sequence alignment", "Phylogenetic tree generation (from molecular sequences)", - "Statistical calculation", - "Global alignment", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "42137e36791652bc", @@ -175183,12 +190515,12 @@ "recombination" ], "tools": [ + "rbc_mafft", + "EMBOSS: transeq101", "fasttree", "hyphy_gard", - "EMBOSS: transeq101", - "rbc_mafft", - "hyphy_absrel", - "EMBOSS: tranalign100" + "EMBOSS: tranalign100", + "hyphy_absrel" ], "update_time": "2020-02-22", "versions": 0 @@ -175198,12 +190530,12 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence alignment analysis", - "Local alignment", "Sequence alignment", - "Global alignment", + "Local alignment", "Multiple sequence alignment", - "Sequence analysis" + "Sequence alignment analysis", + "Sequence analysis", + "Global alignment" ], "edam_topic": [], "id": "f21446cc44da50ce", @@ -175219,8 +190551,8 @@ "s-gene" ], "tools": [ - "EMBOSS: transeq101", "rbc_mafft", + "EMBOSS: transeq101", "EMBOSS: tranalign100" ], "update_time": "2020-02-22", @@ -175231,9 +190563,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Read mapping", - "Genome indexing", "Generation", + "Genome indexing", + "Read mapping", "Sequence alignment" ], "edam_topic": [], @@ -175250,13 +190582,13 @@ "variation" ], "tools": [ - "bwa_mem", - "collapse_dataset", - "snpSift_extractFields", - "snpEff_build_gb", "snpEff", "samtool_filter2", + "snpSift_extractFields", + "collapse_dataset", "lofreq_viterbi", + "bwa_mem", + "snpEff_build_gb", "lofreq_call" ], "update_time": "2020-02-22", @@ -175267,10 +190599,10 @@ "creators": [], "doi": "", "edam_operation": [ + "Phylogenetic tree generation (from molecular sequences)", "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Multiple sequence alignment", "Formatting", - "Phylogenetic tree generation (from molecular sequences)" + "Multiple sequence alignment" ], "edam_topic": [], "id": "d62b6717202f42c9", @@ -175286,15 +190618,15 @@ "mcra" ], "tools": [ - "fasttree", - "ncbi_acc_download", - "collapse_dataset", "picard_NormalizeFasta", - "Cut1", - "tp_sed_tool", "rbc_mafft", + "fasttree", + "collapse_dataset", "Remove beginning1", - "Convert characters1" + "Convert characters1", + "tp_sed_tool", + "ncbi_acc_download", + "Cut1" ], "update_time": "2020-02-22", "versions": 0 @@ -175304,9 +190636,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence assembly visualisation", "Aggregation", - "Genome assembly" + "Genome assembly", + "Sequence assembly visualisation" ], "edam_topic": [], "id": "38d992baf9a2a2bc", @@ -175322,10 +190654,10 @@ "assembly" ], "tools": [ - "spades", "bandage_image", - "unicycler", - "bandage_info" + "spades", + "bandage_info", + "unicycler" ], "update_time": "2020-02-22", "versions": 0 @@ -175335,20 +190667,20 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", + "Sequence contamination filtering", + "Statistical calculation", "Scatter plot plotting", - "Sequence composition calculation", - "Read mapping", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Sequence alignment", "Box-Whisker plot plotting", "Pairwise sequence alignment", - "Sequence contamination filtering", - "Statistical calculation", - "Genome indexing", "Generation", - "Validation" + "Genome indexing", + "Sequence composition calculation", + "Validation", + "Read mapping", + "Data handling" ], "edam_topic": [], "id": "bf80ef6e5f37deb7", @@ -175364,16 +190696,16 @@ "pre-processing" ], "tools": [ - "bwa_mem", - "picard_MergeSamFiles", - "samtools_fastx", - "nanoplot", - "fasterq_dump", - "minimap2", "samtool_filter2", + "samtools_fastx", + "picard_MergeSamFiles", "fastp", + "fasterq_dump", + "nanoplot", "multiqc", - "fastqc" + "bwa_mem", + "fastqc", + "minimap2" ], "update_time": "2020-02-22", "versions": 0 @@ -175383,15 +190715,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Sequence assembly validation", - "Visualisation", "Gene prediction", "Genome annotation", + "Visualisation", "Statistical calculation", "Genome assembly", - "Coding region prediction" + "Sequencing quality control", + "Coding region prediction", + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "39c724282ee008e3", @@ -175404,11 +190736,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "prokka", "trimmomatic", + "spades", "quast", - "prokka", - "fastqc", - "spades" + "fastqc" ], "update_time": "2020-02-13", "versions": 13 @@ -175418,13 +190750,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Filtering", - "Label-free quantification", - "Mass spectrum visualisation", + "Chromatogram visualisation", "Chromatographic alignment", "Peak detection", - "Chromatogram visualisation", - "Validation" + "Label-free quantification", + "Mass spectrum visualisation", + "Validation", + "Filtering" ], "edam_topic": [], "id": "f9e5caaf08a450ec", @@ -175440,14 +190772,14 @@ "lcms" ], "tools": [ - "xcms_merge", - "abims_xcms_fillPeaks", - "abims_CAMERA_annotateDiffreport", - "msnbase_readmsdata", "abims_xcms_xcmsSet", - "xcms_plot_chromatogram", "abims_xcms_retcor", - "abims_xcms_group" + "xcms_plot_chromatogram", + "msnbase_readmsdata", + "abims_xcms_group", + "abims_xcms_fillPeaks", + "xcms_merge", + "abims_CAMERA_annotateDiffreport" ], "update_time": "2019-10-30", "versions": 3 @@ -175471,11 +190803,11 @@ "lcms" ], "tools": [ - "Batch_correction", "wsdl_hmdb", "Univariate", "quality_metrics", - "generic_filter" + "generic_filter", + "Batch_correction" ], "update_time": "2019-10-30", "versions": 1 @@ -175485,13 +190817,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "fa8d1de86aa944a2", @@ -175504,21 +190836,21 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "mothur_classify_otu", "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", - "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", "mothur_make_group", - "mothur_classify_otu", - "mothur_summary_seqs", + "mothur_screen_seqs", + "mothur_pre_cluster", "mothur_taxonomy_to_krona", - "mothur_merge_files", + "mothur_summary_seqs", + "mothur_align_seqs", "mothur_make_contigs", "krona-text", - "mothur_align_seqs" + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2019-06-12", "versions": 16 @@ -175528,18 +190860,18 @@ "creators": [], "doi": "", "edam_operation": [ - "Coding region prediction", - "Sequence assembly", - "Sequence composition calculation", - "Sequencing quality control", - "Variant calling", - "Phylogenetic tree generation", "Gene prediction", "Genome annotation", "Statistical calculation", + "Phylogenetic tree generation", "Genome assembly", - "Phylogenetic tree visualisation", - "Optimisation and refinement" + "Sequence assembly", + "Optimisation and refinement", + "Sequencing quality control", + "Coding region prediction", + "Sequence composition calculation", + "Variant calling", + "Phylogenetic tree visualisation" ], "edam_topic": [], "id": "fa76b66785ce38b8", @@ -175552,14 +190884,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "prokka", "trimmomatic", - "snippy", "velvet", + "spades", "velvetoptimiser", - "shovill", - "prokka", "fastqc", - "spades" + "snippy", + "shovill" ], "update_time": "2019-05-10", "versions": 5 @@ -175569,9 +190901,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "1624a678c6791ca6", @@ -175584,11 +190916,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", + "cuffdiff", "cuffmerge" ], "update_time": "2019-05-07", @@ -175599,9 +190931,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d42df3bb51a94a52", @@ -175614,12 +190946,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-05", @@ -175630,9 +190962,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "b518ee5540ed01fd", @@ -175645,13 +190977,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "fastq_trimmer", - "sort1", "cufflinks", - "fastqc", "Filter1", + "sort1", + "tophat2", + "fastqc", + "fastq_trimmer", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-04", @@ -175662,9 +190994,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "a3efc48b5992374e", @@ -175677,13 +191009,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "fastq_trimmer", - "sort1", "cufflinks", - "fastqc", "Filter1", + "sort1", + "tophat2", + "fastqc", + "fastq_trimmer", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-04", @@ -175694,9 +191026,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d0933b5040adf902", @@ -175709,12 +191041,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", "trimmomatic", - "cuffdiff", "tophat2", - "fastq_trimmer", - "cufflinks", "fastqc", + "fastq_trimmer", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-04", @@ -175725,9 +191057,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "d1b604a5441dc4b0", @@ -175740,13 +191072,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "tp_sort_header_tool", - "cuffdiff", - "tophat2", - "fastq_trimmer", "cufflinks", - "fastqc", "Filter1", + "tophat2", + "tp_sort_header_tool", + "fastqc", + "fastq_trimmer", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-04", @@ -175757,9 +191089,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "79572be1bf642251", @@ -175772,11 +191104,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "fastq_trimmer", "cufflinks", + "tophat2", "fastqc", + "fastq_trimmer", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-04", @@ -175787,9 +191119,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "ec202ccfb5f03d0d", @@ -175802,12 +191134,12 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ + "cufflinks", + "Filter1", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "Filter1", + "cuffdiff", "cuffmerge" ], "update_time": "2019-04-03", @@ -175818,15 +191150,15 @@ "creators": [], "doi": "", "edam_operation": [ - "Data handling", - "Sequence composition calculation", - "Sequencing quality control", - "Sequence alignment", "Statistical calculation", + "Sequence alignment", "Primer removal", + "Sequencing quality control", + "Sequence composition calculation", "Read pre-processing", "Sequence trimming", - "Validation" + "Validation", + "Data handling" ], "edam_topic": [], "id": "bb0feff5d764df60", @@ -175839,11 +191171,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "rna_star", - "rseqc_bam_stat", "multiqc", "fastqc", - "cutadapt" + "rna_star", + "cutadapt", + "rseqc_bam_stat" ], "update_time": "2019-03-29", "versions": 4 @@ -175866,15 +191198,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cut_fr", - "bg_column_arrange_by_header", - "Cut1", + "Paste1", "regex1", - "biom_convert", - "row_means", + "cut_fr", "Remove beginning1", "krona-text", - "Paste1" + "bg_column_arrange_by_header", + "row_means", + "Cut1", + "biom_convert" ], "update_time": "2018-11-26", "versions": 1 @@ -175884,13 +191216,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "177579096e009178", @@ -175904,20 +191236,20 @@ "tags": [], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", - "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", - "mothur_make_group", "mothur_classify_otu", - "mothur_summary_seqs", + "mothur_make_group", + "mothur_screen_seqs", + "mothur_pre_cluster", "mothur_taxonomy_to_krona", - "mothur_merge_files", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_filter_seqs", "krona-text", - "mothur_align_seqs" + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2018-11-09", "versions": 7 @@ -175927,13 +191259,13 @@ "creators": [], "doi": "", "edam_operation": [ - "Taxonomic classification", - "Sequencing quality control", - "Phylogenetic analysis", "Visualisation", "Sequence clustering", + "DNA barcoding", + "Sequencing quality control", + "Phylogenetic analysis", "Sequence read processing", - "DNA barcoding" + "Taxonomic classification" ], "edam_topic": [], "id": "57fe85f947217994", @@ -175947,20 +191279,20 @@ "tags": [], "tools": [ "mothur_make_shared", - "mothur_cluster_split", - "mothur_pre_cluster", - "mothur_screen_seqs", - "mothur_classify_seqs", - "mothur_count_seqs", - "mothur_unique_seqs", - "mothur_filter_seqs", - "mothur_make_group", "mothur_classify_otu", - "mothur_summary_seqs", + "mothur_make_group", + "mothur_screen_seqs", + "mothur_pre_cluster", "mothur_taxonomy_to_krona", - "mothur_merge_files", + "mothur_summary_seqs", + "mothur_align_seqs", + "mothur_filter_seqs", "krona-text", - "mothur_align_seqs" + "mothur_cluster_split", + "mothur_count_seqs", + "mothur_unique_seqs", + "mothur_classify_seqs", + "mothur_merge_files" ], "update_time": "2018-11-07", "versions": 3 @@ -175970,11 +191302,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", - "Read mapping", - "Genome indexing", "Generation", - "Sequence alignment" + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Genome visualisation" ], "edam_topic": [], "id": "8031655d71b59d15", @@ -175987,11 +191319,11 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "bwa_mem", + "rgdifferentialcount", "htseqsams2mxlocal", - "fml_gtf2gff", + "bwa_mem", "jbrowse", - "rgdifferentialcount" + "fml_gtf2gff" ], "update_time": "2018-10-15", "versions": 1 @@ -176001,16 +191333,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Multilocus sequence typing", - "Genome visualisation", "Gene prediction", - "Antimicrobial resistance prediction", "Genome annotation", "Statistical calculation", "Genome assembly", - "Coding region prediction" + "Multilocus sequence typing", + "Sequencing quality control", + "Coding region prediction", + "Sequence composition calculation", + "Genome visualisation", + "Antimicrobial resistance prediction" ], "edam_topic": [], "id": "914330feb75ea9ab", @@ -176023,14 +191355,14 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "abricate", + "prokka", "trimmomatic", - "mlst", "fasta-stats", - "jbrowse", - "prokka", + "spades", + "abricate", "fastqc", - "spades" + "jbrowse", + "mlst" ], "update_time": "2018-09-03", "versions": 2 @@ -176040,11 +191372,11 @@ "creators": [], "doi": "", "edam_operation": [ - "Genome visualisation", "Gene prediction", + "Coding region prediction", "Genome annotation", "Genome assembly", - "Coding region prediction" + "Genome visualisation" ], "edam_topic": [], "id": "87cdeb05b1ebeab0", @@ -176101,10 +191433,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "cufflinks", "Filter1", + "cufflinks", + "tophat2", + "cuffdiff", "cuffmerge" ], "update_time": "2018-03-28", @@ -176126,10 +191458,10 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "cuffdiff", - "tophat2", - "cufflinks", "Filter1", + "cufflinks", + "tophat2", + "cuffdiff", "cuffmerge" ], "update_time": "2018-03-28", @@ -176140,16 +191472,16 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Read mapping", + "Statistical calculation", + "Sequence alignment", "Sequencing quality control", "Formatting", - "Variant calling", - "Sequence alignment", - "Statistical calculation", - "Mapping", + "Generation", "Genome indexing", - "Generation" + "Sequence composition calculation", + "Variant calling", + "Read mapping", + "Mapping" ], "edam_topic": [], "id": "3d5deed70ac9bde4", @@ -176167,22 +191499,22 @@ "illumina" ], "tools": [ - "bwa_mem", - "gatk_realigner_target_creator", - "vcftools_isec", - "trimmomatic", - "bam_to_sam", + "bowtie2", "gatk2_realigner_target_creator", + "freebayes", + "snpEff", + "trimmomatic", "gatk_indel_realigner", - "gatk2_indel_realigner", "samtools_sort", - "freebayes", + "gatk2_indel_realigner", + "picard_AddOrReplaceReadGroups", + "bam_to_sam", + "bedtools_intersectbed", "gatk2_unified_genotyper", - "snpEff", + "vcftools_isec", + "bwa_mem", "fastqc", - "bowtie2", - "bedtools_intersectbed", - "picard_AddOrReplaceReadGroups" + "gatk_realigner_target_creator" ], "update_time": "2017-07-14", "versions": 9 @@ -176192,9 +191524,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "60c5675ed2f4a7d8", @@ -176207,13 +191539,13 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastq_groomer", + "cufflinks", "trimmomatic", - "cuffdiff", "tophat2", - "cufflinks", "fastqc", - "cuffmerge" + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2017-05-18", "versions": 1 @@ -176223,9 +191555,9 @@ "creators": [], "doi": "", "edam_operation": [ - "Sequencing quality control", + "Sequence composition calculation", "Statistical calculation", - "Sequence composition calculation" + "Sequencing quality control" ], "edam_topic": [], "id": "39bb22274ede7500", @@ -176238,15 +191570,15 @@ "source": "https://usegalaxy.org.au", "tags": [], "tools": [ - "fastq_groomer", + "cufflinks", + "Filter1", + "sort1", "trimmomatic", - "cuffdiff", "tophat2", - "sort1", - "cufflinks", "fastqc", - "Filter1", - "cuffmerge" + "cuffdiff", + "cuffmerge", + "fastq_groomer" ], "update_time": "2017-03-30", "versions": 0 diff --git a/communities/microgalaxy/metadata/workflow_status.tsv b/communities/microgalaxy/metadata/workflow_status.tsv new file mode 100644 index 00000000..38db095c --- /dev/null +++ b/communities/microgalaxy/metadata/workflow_status.tsv @@ -0,0 +1,150 @@ +Link Name Source Projects Creators Creation time Update time To keep Deprecated +https://workflowhub.eu/workflows/1043?version=7 bacterial-genome-assembly/main WorkflowHub Intergalactic Workflow Commission (IWC) Abromics None, Pierre Marin, Clea Siguret 2024-11-26 2024-11-26 True False +https://workflowhub.eu/workflows/1052?version=8 quality-and-contamination-control/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-11-23 2024-11-23 True False +https://workflowhub.eu/workflows/1050?version=9 bacterial_genome_annotation/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-10-26 2024-10-26 True False +https://workflowhub.eu/workflows/1049?version=7 amr_gene_detection/main WorkflowHub Intergalactic Workflow Commission (IWC) ABRomics None, Pierre Marin, Clea Siguret 2024-10-26 2024-10-27 True False +https://workflowhub.eu/workflows/439?version=2 pox-virus-amplicon/main WorkflowHub Intergalactic Workflow Commission (IWC) Viktoria Isabel Schwarz, Wolfgang Maier 2024-06-22 2024-06-22 True False +https://workflowhub.eu/workflows/406?version=1 GTN Training - Antibiotic Resistance Detection WorkflowHub Galaxy Training Network Saskia Hiltemann, Willem de Koning 2022-11-24 2023-02-13 True False +https://workflowhub.eu/workflows/103?version=1 3: Plant virus exploration WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2023-02-13 True False +https://workflowhub.eu/workflows/102?version=1 2: Plant virus confirmation WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2023-02-13 True False +https://workflowhub.eu/workflows/124?version=1 1: Plant virus detection with kraken2 (SE) WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-06-17 2023-02-13 True False +https://workflowhub.eu/workflows/101?version=1 1: Plant virus detection with kraken2 (PE) WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2023-02-13 True False +https://workflowhub.eu/workflows/1199?version=2 Taxonomy classification using Kraken2 and Bracken WorkflowHub QCIF Bioinformatics Valentine Murigneux, Mike Thang 2024-12-10 2024-12-10 True False +https://workflowhub.eu/workflows/624?version=1 Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub QCIF Bioinformatics Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut 2023-10-26 2024-04-05 True False +https://workflowhub.eu/workflows/653?version=1 Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/652?version=1 Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/651?version=1 Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/650?version=1 Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/648?version=1 Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/649?version=1 Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub QCIF Bioinformatics Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi 2023-11-09 2023-11-09 True False +https://workflowhub.eu/workflows/470?version=1 Workflow 4: Staramr WorkflowHub Seq4AMR 2023-05-11 2024-09-09 True False +https://workflowhub.eu/workflows/1189?version=2 AMR-Pathfinder WorkflowHub Seq4AMR, ErasmusMC Clinical Bioinformatics Helena Rasche, Dennis Dollée, Birgit Rijvers 2024-11-14 2024-11-14 True False +https://dev.workflowhub.eu/workflows/1366?version=1 Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub Galaxy Training Network 2024-10-07 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1133?version=1 Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1129?version=1 Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1125?version=1 Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1121?version=1 Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1117?version=1 Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1112?version=1 Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1107?version=1 Copy Of GTN Training - Antibiotic Resistance Detection dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1105?version=2 Building an amplicon sequence variant (ASV) table from 16S data using DADA2 dev.WorkflowHub Galaxy Training Network 2024-07-16 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1101?version=1 Training: 16S rRNA Sequencing With Mothur: Main Tutorial dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1097?version=1 Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1095?version=1 Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1080?version=1 Workflow 3: Functional Information (quick) dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1070?version=1 Amplicon Tutorial dev.WorkflowHub Galaxy Training Network 2024-06-25 2024-10-07 True False +https://dev.workflowhub.eu/workflows/1067?version=1 "WGS Part In ""Analyses Of Metagenomics Data - 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False +https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 Apollo Load Test https://usegalaxy.eu 2023-12-14 2023-12-14 True False +https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu 2023-12-14 2023-12-14 False False +https://usegalaxy.eu/published/workflow?id=152223c8aed27357 Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 2023-12-14 2023-12-14 True False +https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 Mtb phylogeny https://usegalaxy.eu 2023-12-14 2023-12-14 False False +https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 From VCFs to SNP distance matrix https://usegalaxy.eu 2023-12-14 2023-12-14 True False +https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 From Fastqs to VCFs and BAMs https://usegalaxy.eu 2023-12-14 2023-12-14 True False +https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu 2023-12-14 2023-12-14 True False +https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu Peter van Heusden 2023-12-14 2023-12-14 False False +https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 Compute Allel Frequency Table from paired reads https://usegalaxy.eu 2023-12-13 2023-12-13 True False +https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 2023-10-27 2023-12-13 True False +https://usegalaxy.eu/published/workflow?id=437704898229dfb6 MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 2023-12-12 2023-12-13 False False +https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 MGnify amplicon QC https://usegalaxy.eu 2023-12-13 2023-12-13 False False +https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 2021-11-10 2023-12-07 False False +https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 2021-11-01 2023-12-07 False False +https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 2021-11-01 2023-12-07 False False +https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu 2022-06-29 2023-12-07 False False +https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu 2022-09-03 2023-12-07 False False +https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 pAllori ASiam Functional Information MT https://usegalaxy.eu Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr 2023-07-07 2023-07-07 False False +https://usegalaxy.eu/published/workflow?id=05f5f040337786bf pAllori ASiam Community Profile MT https://usegalaxy.eu Engy Nasr, Bérénice Batut 2023-06-30 2023-07-06 False False +https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a pAllori ASiam Preprocessing MT https://usegalaxy.eu Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr 2023-06-30 2023-07-06 False False +https://usegalaxy.eu/published/workflow?id=96d198ed953449fd MetaP https://usegalaxy.eu 2020-01-30 2023-03-16 False False +https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e MetaG_extended https://usegalaxy.eu 2023-02-10 2023-03-16 False False +https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b MetaT https://usegalaxy.eu 2020-01-27 2023-02-27 False False +https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-11-28 2024-11-28 False False +https://usegalaxy.org/published/workflow?id=6d778eeb176d563c Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-10-31 2024-10-31 False False +https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org/published/workflow?id=2d3063882d8239ff Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-07-03 2024-07-03 False False +https://usegalaxy.org/published/workflow?id=e55593af91337a05 PathoGFAIR (imported from uploaded file) https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-07-03 2024-07-03 False False +https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 Taxonomy Profiling and Visualization with Krona https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 Gene-based Pathogen Identification https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 Allele-based Pathogen Identification https://usegalaxy.org Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org/published/workflow?id=574e42683dc3961b Nanopore Preprocessing https://usegalaxy.org Bérénice Batut, Engy Nasr, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-10-31 2024-10-31 False False +https://usegalaxy.org.au/published/workflow?id=131636a795bac485 Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 Nanopore Preprocessing (release v0.1) https://usegalaxy.org.au Bérénice Batut, Engy Nasr, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-09-19 2024-09-19 False False +https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c PathoGFAIR (imported from uploaded file) https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-07-03 2024-07-03 False False +https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-07-03 2024-07-03 False False +https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad Allele-based Pathogen Identification https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 Gene-based Pathogen Identification https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 Taxonomy Profiling and Visualization with Krona https://usegalaxy.org.au Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-25 2024-06-25 False False +https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b Nanopore Preprocessing https://usegalaxy.org.au Bérénice Batut, Engy Nasr, Paul Zierep 2024-06-25 2024-06-25 False False diff --git a/communities/microgalaxy/resources/curated_workflows.tsv b/communities/microgalaxy/resources/curated_workflows.tsv new file mode 100644 index 00000000..967d43fb --- /dev/null +++ b/communities/microgalaxy/resources/curated_workflows.tsv @@ -0,0 +1,83 @@ +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=7 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2024-11-26 2024-11-26 7 7 7.0 bandage_info, bandage_image, quast, tooldistillator, tooldistillator_summarize, refseq_masher_matches, shovill Visualisation, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Parsing, Data handling GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=8 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-11-23 2024-11-23 8 8 6.0 recentrifuge, kraken2, fastp, tooldistillator, est_abundance, tooldistillator_summarize Sequence contamination filtering, Statistical calculation, Expression analysis, Parsing, Sequencing quality control, Cross-assembly, Data handling, Taxonomic classification GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2024-10-26 2024-10-26 9 9 6.0 bakta, tooldistillator_summarize, tooldistillator, isescan, integron_finder, plasmidfinder Genome annotation, Sequence motif recognition, Genome assembly, Multilocus sequence typing, Parsing, Scaffolding, Protein feature detection, Structural variation detection, Nucleic acid feature detection, Data handling GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=7 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2024-10-26 2024-10-27 7 7 5.0 abricate, tooldistillator, tooldistillator_summarize, amrfinderplus, staramr_search Data handling, Parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=2 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2024-06-22 2024-06-22 2 2 40.0 " + __APPLY_RULES__, samtools_merge, tp_cat, + __ZIP_COLLECTION__, + __FLATTEN__, + param_value_from_file, + Grep1, qualimap_bamqc, collection_element_identifiers, EMBOSS: maskseq51, multiqc, bwa_mem, ivar_trim, samtools_view, fasta_compute_length, + Cut1, + __SORTLIST__, compose_text_param, ivar_consensus, samtools_stats, fastp, split_file_to_collection, + __FILTER_FAILED_DATASETS__, tp_sed_tool, datamash_ops" Sequence contamination filtering, Sequence alignment, Sequencing quality control, Local alignment, Generation, Genome indexing, Sequence alignment analysis, Sequence analysis, Global alignment, Validation, Read mapping MIT Intergalactic Workflow Commission (IWC) True False +GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2023-02-13 1 1 12.0 miniasm, racon, PlasFlow, nanoplot, gfa_to_fa, bandage_image, unicycler, minimap2, staramr_search Genome assembly, Scatter plot plotting, Sequence assembly visualisation, Mapping assembly, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, De-novo assembly, Sequence analysis Microbiology CC-BY-4.0 Galaxy Training Network True False +3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2023-02-13 1 1 2.0 fastp, shovill Sequence contamination filtering, Sequencing quality control, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2023-02-13 1 1 7.0 samtools_stats, minimap2, ngsutils_bam_filter, ncbi_blastn_wrapper, picard_SamToFastq, fasta_merge_files_and_filter_unique_sequences, shovill Sequence contamination filtering, Pairwise sequence alignment, Read pre-processing, Genome assembly, Variant calling, Sequencing quality control, Formatting Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2023-02-13 1 1 3.0 taxonomy_krona_chart, kraken2, Kraken2Tax Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2023-02-13 1 1 3.0 taxonomy_krona_chart, kraken2, Kraken2Tax Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "Prepare alpha diversity summary file (paste sample identifiers and Simpson results) +Paste1, collection_element_identifiers, add_line_to_file, kraken2, regex1, krakentools_kreport2krona, cat_multiple, taxonomy_krona_chart, Prepare alpha diversity summary file +Paste1, collection_column_join, krakentools_combine_kreports, est_abundance, krakentools_beta_diversity, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" +Show tail1, Extract column name and fraction_total_reads from Bracken report +Cut1, __RELABEL_FROM_FILE__, Prepare alpha diversity summary file (paste Simpson and Fisher results) +Paste1, krakentools_alpha_diversity" Visualisation, Statistical calculation, Taxonomic classification, Aggregation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False +Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2024-04-05 1 1 17.0 , humann2_renorm_table, taxonomy_krona_chart, humann2_regroup_table, merge_metaphlan_tables, metaphlan2, metaphlan2krona, humann2, Cut1 Phylogenetic tree analysis, Visualisation, Nucleic acid sequence analysis Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False +Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 4.0 mothur_heatmap_sim, mothur_dist_shared, mothur_tree_shared, newick_display Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 3.0 mothur_rarefaction_single, XY_Plot_1, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_make_shared, mothur_classify_otu, mothur_sub_sample, mothur_cluster_split, mothur_count_groups Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_count_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_screen_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 9.0 mothur_pre_cluster, mothur_screen_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_remove_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2024-09-09 1 1 10.0 shovill, collapse_dataset, tp_find_and_replace, abricate, hamronize_summarize, staramr_search, hamronize_tool Genome assembly, Data handling, Parsing, Antimicrobial resistance prediction GPL-3.0 Seq4AMR True False +AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2024-11-14 2 2 36.0 , collapse_dataset, tp_find_and_replace, abricate, Cut1, Grep1, __APPLY_RULES__, staramr_search, __MERGE_COLLECTION__, hamronize_summarize, addValue, hamronize_tool, cat1, tp_split_on_column, cat_multi_datasets, tp_text_file_with_recurring_lines, datamash_ops, cast, shovill Genome assembly, Data handling, Parsing, Antimicrobial resistance prediction MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False +Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub 1366 https://dev.workflowhub.eu/workflows/1366?version=1 fungi, gtn, galaxy, lotus2, ecology, metagenomics 2024-10-07 2024-10-07 1 1 1.0 lotus2 DNA barcoding, Sequence feature detection MIT Galaxy Training Network True False +Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1133 https://dev.workflowhub.eu/workflows/1133?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_make_shared, mothur_classify_otu, mothur_remove_groups, mothur_sub_sample, mothur_cluster_split, mothur_count_groups Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1129 https://dev.workflowhub.eu/workflows/1129?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_rarefaction_single, XY_Plot_1, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1125 https://dev.workflowhub.eu/workflows/1125?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 4.0 mothur_make_shared, mothur_cluster, mothur_rarefaction_single, mothur_dist_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1121 https://dev.workflowhub.eu/workflows/1121?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 5.0 mothur_count_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_screen_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1117 https://dev.workflowhub.eu/workflows/1117?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_dist_shared, mothur_tree_shared, collapse_dataset, mothur_venn, mothur_heatmap_sim, newick_display Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1112 https://dev.workflowhub.eu/workflows/1112?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 9.0 mothur_pre_cluster, mothur_screen_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_remove_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Copy Of GTN Training - Antibiotic Resistance Detection dev.WorkflowHub 1107 https://dev.workflowhub.eu/workflows/1107?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 12.0 miniasm, racon, PlasFlow, nanoplot, gfa_to_fa, bandage_image, unicycler, minimap2, staramr_search Genome assembly, Scatter plot plotting, Sequence assembly visualisation, Mapping assembly, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, De-novo assembly, Sequence analysis CC-BY-4.0 Galaxy Training Network True False +Building an amplicon sequence variant (ASV) table from 16S data using DADA2 dev.WorkflowHub 1105 https://dev.workflowhub.eu/workflows/1105?version=2 gtn, galaxy, microbiome 2024-07-16 2024-10-07 2 2 21.0 dada2_makeSequenceTable, collection_element_identifiers, cat1, dada2_assignTaxonomyAddspecies, Add_a_column1, dada2_plotQualityProfile, dada2_dada, tp_head_tool, dada2_removeBimeraDenovo, dada2_seqCounts, dada2_filterAndTrim, tp_replace_in_line, __SORTLIST__, dada2_learnErrors, dada2_mergePairs, tp_replace_in_column, phyloseq_from_dada2, __UNZIP_COLLECTION__ Visualisation, Deposition, Analysis, Variant calling, DNA barcoding MIT Galaxy Training Network True False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial dev.WorkflowHub 1101 https://dev.workflowhub.eu/workflows/1101?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 38.0 mothur_screen_seqs, mothur_sub_sample, mothur_cluster, mothur_make_biom, newick_display, mothur_count_groups, mothur_classify_seqs, mothur_dist_shared, mothur_tree_shared, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_seq_error, mothur_unique_seqs, mothur_classify_otu, mothur_align_seqs, mothur_summary_seqs, mothur_venn, taxonomy_krona_chart, mothur_filter_seqs, mothur_remove_seqs, mothur_summary_single, mothur_cluster_split, mothur_count_seqs, mothur_make_shared, mothur_remove_groups, mothur_pre_cluster, mothur_get_groups, mothur_chimera_vsearch, mothur_heatmap_sim, mothur_rarefaction_single, mothur_make_contigs, mothur_dist_seqs, XY_Plot_1 Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub 1097 https://dev.workflowhub.eu/workflows/1097?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 8.0 Filter1, kraken2, krakentools_kreport2krona, fastp, taxonomy_krona_chart, porechop, fastqc Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Taxonomic classification, Sequencing quality control, Aggregation MIT Galaxy Training Network True False +Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub 1095 https://dev.workflowhub.eu/workflows/1095?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 10.0 kraken_biom, kraken2, krakentools_kreport2krona, interactive_tool_phinch, taxonomy_krona_chart, est_abundance, metaphlan, interactive_tool_pavian, __UNZIP_COLLECTION__ Visualisation, Statistical calculation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Aggregation MIT Galaxy Training Network True False +Workflow 3: Functional Information (quick) dev.WorkflowHub 1080 https://dev.workflowhub.eu/workflows/1080?version=1 gtn, galaxy, asaim, metagenomics 2024-06-25 2024-10-07 1 1 12.0 humann_regroup_table, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Grep1, humann_unpack_pathways, humann_split_stratified_table, Cut1, humann_renorm_table Species frequency estimation, Phylogenetic analysis, Taxonomic classification MIT Galaxy Training Network True False +Amplicon Tutorial dev.WorkflowHub 1070 https://dev.workflowhub.eu/workflows/1070?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 17.0 mothur_make_shared, mothur_classify_otu, mothur_make_group, mothur_screen_seqs, mothur_pre_cluster, mothur_summary_seqs, mothur_align_seqs, mothur_filter_seqs, mothur_make_biom, krona-text, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_classify_seqs, mothur_merge_files Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" dev.WorkflowHub 1067 https://dev.workflowhub.eu/workflows/1067?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 7.0 humann2_renorm_table, taxonomy_krona_chart, humann2_regroup_table, metaphlan2, metaphlan2krona, humann2 Visualisation CC-BY-4.0 Galaxy Training Network True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads dev.WorkflowHub 1064 https://dev.workflowhub.eu/workflows/1064?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 11.0 kraken2, fastp, multiqc, tp_replace_in_line, porechop, taxonomy_krona_chart, Remove beginning1, fastqc, datamash_reverse Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Validation, Sequencing quality control, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1060 https://dev.workflowhub.eu/workflows/1060?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2024-12-20 2 2 collapse_dataset, humann, fastq_paired_end_interlacer, humann_unpack_pathways, collection_column_join, est_abundance, metaphlan, add_line_to_file, humann_regroup_table, bowtie2, collection_element_identifiers, humann_rename_table, sort1, krakentools_kreport2krona, csv_to_tabular, tp_easyjoin_tool, __UNZIP_COLLECTION__, krakentools_alpha_diversity, cat1, kraken2, taxpasta, tp_replace_in_line, taxonomy_krona_chart, __ZIP_COLLECTION__, datamash_transpose, fastp, Remove beginning1, tp_sed_tool, tp_text_file_with_recurring_lines, tp_awk_tool, humann_renorm_table Sequence contamination filtering, Statistical calculation, Nucleic acid sequence analysis, Visualisation, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Formatting, Aggregation, Standardisation and normalisation, Species frequency estimation, Conversion, Read mapping, Taxonomic classification MIT True False +ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 humann2_renorm_table, combine_metaphlan2_humann2, Grep1, fastq_paired_end_interlacer, metaphlan2krona, fastqc, humann2, multiqc, metaphlan2, group_humann2_uniref_abundances_to_go, humann2_genefamilies_genus_level, tp_sort_header_tool, cutadapt, export2graphlan, bg_sortmerna, taxonomy_krona_chart, humann2_unpack_pathways, graphlan_annotate, graphlan, Grouping1, format_metaphlan2_output Visualisation, Primer removal, Sequencing quality control, Formatting, Sequence similarity search, Conversion, Phylogenetic inference, Sequence trimming, Statistical calculation, Sequence comparison, Phylogenetic tree editing, Sequence composition calculation, Read pre-processing, Sequence alignment analysis, Validation, Phylogenetic tree visualisation, Taxonomic classification MIT True False +MAGs building with individual assembly https://usegalaxy.eu 0563f58718be932d https://usegalaxy.eu/published/workflow?id=0563f58718be932d Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler name:fairymags, name:microgalaxy 2024-12-20 2024-12-20 1 1 fastq_paired_end_joiner, checkm_plot, checkm_lineage_wf, collection_column_join, concoct_cut_up_fasta, bowtie2, drep_dereplicate, samtools_sort, multiqc, concoct_merge_cut_up_clustering, gtdbtk_classify_wf, semibin, quast, __FLATTEN__, __UNZIP_COLLECTION__, concoct_extract_fasta_bins, metabat2, megahit, concoct, metabat2_jgi_summarize_bam_contig_depths, Fasta_to_Contig2Bin, coverm_genome, das_tool, maxbin2, concoct_coverage_table Genome annotation, Read binning, Visualisation, Genome comparison, Sequence assembly, Sequencing quality control, Sequence assembly validation, Genome alignment, Read mapping, Statistical calculation, Sequence clustering, Genome assembly, Local alignment, Query and retrieval, Sequence composition calculation, Validation, Taxonomic classification MIT True False +MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 kallisto_quant, bg_sortmerna, trim_galore, collection_column_join, fastqc, __UNZIP_COLLECTION__ Statistical calculation, Primer removal, Sequencing quality control, Sequence comparison, Sequence similarity search, Read pre-processing, Sequence composition calculation, Sequence alignment analysis, Sequence trimming, Gene expression profiling MIT True False +MGnify's amplicon pipeline v5.0 https://usegalaxy.eu 02f90a96d01fed4f https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2024-05-06 2024-12-16 103 103 __MERGE_COLLECTION__, fastq_dl, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, tp_awk_tool Apache-2.0 True False +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 regexColumn1, cat1, Filter1, Add_a_column1, rbc_mafft, collapse_dataset, tab2fasta, bg_diamond_view, rapidnj, bg_diamond, gops_intersect_1, join1, Cut1, tp_split_on_column Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment True False +MGnify's amplicon pipeline v5.0 - Quality control SE https://usegalaxy.eu b7166aff73e5d81c https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-03-25 2024-11-26 16 16 fastq_filter, fastq_to_fasta_python, trimmomatic, tp_find_and_replace, prinseq, multiqc, cshl_fasta_formatter, fastqc Sequence contamination filtering, Read pre-processing, Sequence composition calculation, Statistical calculation, Sequence trimming, Validation, Sequencing quality control Apache-2.0 True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 featurecounts, multiqc, __FILTER_FAILED_DATASETS__, umi_tools_extract, collection_column_join, fastqc, rna_star Sequence composition calculation, Statistical calculation, Validation, Sequence alignment, RNA-Seq quantification, Read summarisation, Sequencing quality control MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 sqlite_to_tabular, unipept, search_gui, query_tabular, peptide_shaker Visualisation, Prediction and recognition MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 __EXTRACT_DATASET__, __BUILD_LIST__, Grep1, map_param_value, __FILTER_EMPTY_DATASETS__ MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 msconvert, Filter1, regex1, query_tabular, unipept, tp_replace_in_line, search_gui, Remove beginning1, tp_replace_in_column, flashlfq, Cut1, peptide_shaker Visualisation, Prediction and recognition, Filtering, Formatting, Label-free quantification MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_expand, metaquantome_stat, metaquantome_sample, metaquantome_filter, metaquantome_viz, metaquantome_db Visualisation, Indexing, Differential protein expression analysis, Statistical inference, Functional clustering, Query and retrieval, Quantification, Principal component visualisation, Heat map generation, Filtering MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 ampvis2_heatmap, ampvis2_ordinate, unzip, kraken2, trimmomatic, krakentools_kreport2krona, multiqc, taxonomy_krona_chart, ampvis2_load, collection_column_join, __FLATTEN__, fastqc, tp_cut_tool, cutadapt, lotus2 Visualisation, Statistical calculation, Analysis, Primer removal, Sequencing quality control, DNA barcoding, Aggregation, Sequence composition calculation, Read pre-processing, Sequence trimming, Validation, Sequence feature detection, Taxonomic classification MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, fastq_to_tabular, filter_tabular, recentrifuge, kraken2, seq_filter_by_id Expression analysis, Read mapping, Cross-assembly, Taxonomic classification MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 bowtie2, multiqc, featurecounts RNA-Seq quantification, Validation, Sequencing quality control, Read mapping, Read summarisation MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control MIT True False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.eu 64abcddeb516a712 https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 - Quality control PE https://usegalaxy.eu f9648091c06171cd https://usegalaxy.eu/published/workflow?id=f9648091c06171cd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-27 2024-10-25 16 16 fastq_filter, fastq_to_fasta_python, trimmomatic, tp_find_and_replace, prinseq, mgnify_seqprep, fastp, multiqc, cshl_fasta_formatter, fastqc, __UNZIP_COLLECTION__ Sequence contamination filtering, Statistical calculation, Sequencing quality control, Nucleic acid design, Read pre-processing, Sequence composition calculation, Sequence trimming, Validation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - rRNA prediction https://usegalaxy.eu 0c3eee883f5ab977 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2024-05-06 2024-10-25 31 31 collection_element_identifiers, gops_concat_1, infernal_cmsearch, taxonomy_krona_chart, cmsearch_deoverlap, cshl_fasta_formatter, __FILTER_EMPTY_DATASETS__, biom_convert, mapseq, query_tabular, bedtools_getfastabed, __FILTER_FROM_FILE__, tp_awk_tool k-mer counting, Mapping, Visualisation, Alignment, Nucleic acid feature detection, Formatting, Comparison Apache-2.0 True False +Taxonomic abundance summary tables for a specified taxonomic rank https://usegalaxy.eu b57fa7ac24a1e777 https://usegalaxy.eu/published/workflow?id=b57fa7ac24a1e777 Rand Zoabi mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-09-27 2024-10-25 1 1 filter_tabular, map_param_value, Grouping1, collection_column_join, tp_awk_tool MIT True False +MGnify's amplicon pipeline v5.0 - ITS https://usegalaxy.eu 169327ba670607d1 https://usegalaxy.eu/published/workflow?id=169327ba670607d1 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-06 2024-10-25 24 24 collection_element_identifiers, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, bedtools_maskfastabed, biom_convert, mapseq, __FILTER_FROM_FILE__, tp_awk_tool k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False +MGnify amplicon summary tables https://usegalaxy.eu 05dc8f4321a42cdc https://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdc Rand Zoabi mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-22 2024-10-25 69 69 filter_tabular, collection_column_join, Grouping1, query_tabular, tp_awk_tool MIT True False +Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microgalaxy 2023-10-10 2024-03-15 128 128 interactive_tool_jupyter_notebook, __BUILD_LIST__ True False +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 collapse_dataset, Cut1, tp_cat, Grep1, random_lines1, join1, tp_grep_tool, Filter1, bedtools_complementbed, tp_sort_header_tool, addValue, fasta_compute_length, cat1, lastz_wrapper_2, bedtools_sortbed, fasta_filter_by_length, mergeCols1, bedtools_intersectbed, tp_sed_tool, datamash_ops Sequence alignment, Read mapping, Mapping True False +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 regexColumn1, cat1, Filter1, Add_a_column1, rbc_mafft, collapse_dataset, tab2fasta, bg_diamond_view, rapidnj, bg_diamond, gops_intersect_1, join1, Cut1, tp_split_on_column Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment True False +Apollo Load Test 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mode 100644 index 00000000..19420d55 --- /dev/null +++ b/communities/microgalaxy/resources/tag_filtered_workflows.tsv @@ -0,0 +1,163 @@ +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=7 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2024-11-26 2024-11-26 7 7 7.0 bandage_info, bandage_image, quast, tooldistillator, tooldistillator_summarize, refseq_masher_matches, shovill Visualisation, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Parsing, Data handling GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=8 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-11-23 2024-11-23 8 8 6.0 recentrifuge, kraken2, fastp, tooldistillator, est_abundance, tooldistillator_summarize Sequence contamination filtering, Statistical calculation, Expression analysis, Parsing, Sequencing quality control, Cross-assembly, Data handling, Taxonomic classification GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2024-10-26 2024-10-26 9 9 6.0 bakta, tooldistillator_summarize, tooldistillator, isescan, integron_finder, plasmidfinder Genome annotation, Sequence motif recognition, Genome assembly, Multilocus sequence typing, Parsing, Scaffolding, Protein feature detection, Structural variation detection, Nucleic acid feature detection, Data handling GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=7 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2024-10-26 2024-10-27 7 7 5.0 abricate, tooldistillator, tooldistillator_summarize, amrfinderplus, staramr_search Data handling, Parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=2 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2024-06-22 2024-06-22 2 2 40.0 " + __APPLY_RULES__, samtools_merge, tp_cat, + __ZIP_COLLECTION__, + __FLATTEN__, + param_value_from_file, + Grep1, qualimap_bamqc, collection_element_identifiers, EMBOSS: maskseq51, multiqc, bwa_mem, ivar_trim, samtools_view, fasta_compute_length, + Cut1, + __SORTLIST__, compose_text_param, ivar_consensus, samtools_stats, fastp, split_file_to_collection, + __FILTER_FAILED_DATASETS__, tp_sed_tool, datamash_ops" Sequence contamination filtering, Sequence alignment, Sequencing quality control, Local alignment, Generation, Genome indexing, Sequence alignment analysis, Sequence analysis, Global alignment, Validation, Read mapping MIT Intergalactic Workflow Commission (IWC) True False +GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2023-02-13 1 1 12.0 miniasm, racon, PlasFlow, nanoplot, gfa_to_fa, bandage_image, unicycler, minimap2, staramr_search Genome assembly, Scatter plot plotting, Sequence assembly visualisation, Mapping assembly, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, De-novo assembly, Sequence analysis Microbiology CC-BY-4.0 Galaxy Training Network True False +3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2023-02-13 1 1 2.0 fastp, shovill Sequence contamination filtering, Sequencing quality control, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2023-02-13 1 1 7.0 samtools_stats, minimap2, ngsutils_bam_filter, ncbi_blastn_wrapper, picard_SamToFastq, fasta_merge_files_and_filter_unique_sequences, shovill Sequence contamination filtering, Pairwise sequence alignment, Read pre-processing, Genome assembly, Variant calling, Sequencing quality control, Formatting Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2023-02-13 1 1 3.0 taxonomy_krona_chart, kraken2, Kraken2Tax Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2023-02-13 1 1 3.0 taxonomy_krona_chart, kraken2, Kraken2Tax Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "Prepare alpha diversity summary file (paste sample identifiers and Simpson results) +Paste1, collection_element_identifiers, add_line_to_file, kraken2, regex1, krakentools_kreport2krona, cat_multiple, taxonomy_krona_chart, Prepare alpha diversity summary file +Paste1, collection_column_join, krakentools_combine_kreports, est_abundance, krakentools_beta_diversity, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" +Show tail1, Extract column name and fraction_total_reads from Bracken report +Cut1, __RELABEL_FROM_FILE__, Prepare alpha diversity summary file (paste Simpson and Fisher results) +Paste1, krakentools_alpha_diversity" Visualisation, Statistical calculation, Taxonomic classification, Aggregation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False +Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2024-04-05 1 1 17.0 , humann2_renorm_table, taxonomy_krona_chart, humann2_regroup_table, merge_metaphlan_tables, metaphlan2, metaphlan2krona, humann2, Cut1 Phylogenetic tree analysis, Visualisation, Nucleic acid sequence analysis Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False +Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 4.0 mothur_heatmap_sim, mothur_dist_shared, mothur_tree_shared, newick_display Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 3.0 mothur_rarefaction_single, XY_Plot_1, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_make_shared, mothur_classify_otu, mothur_sub_sample, mothur_cluster_split, mothur_count_groups Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_count_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_screen_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 9.0 mothur_pre_cluster, mothur_screen_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_remove_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 QCIF Bioinformatics True False +Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2024-09-09 1 1 10.0 shovill, collapse_dataset, tp_find_and_replace, abricate, hamronize_summarize, staramr_search, hamronize_tool Genome assembly, Data handling, Parsing, Antimicrobial resistance prediction GPL-3.0 Seq4AMR True False +AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2024-11-14 2 2 36.0 , collapse_dataset, tp_find_and_replace, abricate, Cut1, Grep1, __APPLY_RULES__, staramr_search, __MERGE_COLLECTION__, hamronize_summarize, addValue, hamronize_tool, cat1, tp_split_on_column, cat_multi_datasets, tp_text_file_with_recurring_lines, datamash_ops, cast, shovill Genome assembly, Data handling, Parsing, Antimicrobial resistance prediction MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False +Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' dev.WorkflowHub 1366 https://dev.workflowhub.eu/workflows/1366?version=1 fungi, gtn, galaxy, lotus2, ecology, metagenomics 2024-10-07 2024-10-07 1 1 1.0 lotus2 DNA barcoding, Sequence feature detection MIT Galaxy Training Network True False +Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1133 https://dev.workflowhub.eu/workflows/1133?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_make_shared, mothur_classify_otu, mothur_remove_groups, mothur_sub_sample, mothur_cluster_split, mothur_count_groups Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1129 https://dev.workflowhub.eu/workflows/1129?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_rarefaction_single, XY_Plot_1, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1125 https://dev.workflowhub.eu/workflows/1125?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 4.0 mothur_make_shared, mothur_cluster, mothur_rarefaction_single, mothur_dist_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1121 https://dev.workflowhub.eu/workflows/1121?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 5.0 mothur_count_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_screen_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1117 https://dev.workflowhub.eu/workflows/1117?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 6.0 mothur_dist_shared, mothur_tree_shared, collapse_dataset, mothur_venn, mothur_heatmap_sim, newick_display Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1112 https://dev.workflowhub.eu/workflows/1112?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 9.0 mothur_pre_cluster, mothur_screen_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_remove_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Copy Of GTN Training - Antibiotic Resistance Detection dev.WorkflowHub 1107 https://dev.workflowhub.eu/workflows/1107?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 12.0 miniasm, racon, PlasFlow, nanoplot, gfa_to_fa, bandage_image, unicycler, minimap2, staramr_search Genome assembly, Scatter plot plotting, Sequence assembly visualisation, Mapping assembly, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, De-novo assembly, Sequence analysis CC-BY-4.0 Galaxy Training Network True False +Building an amplicon sequence variant (ASV) table from 16S data using DADA2 dev.WorkflowHub 1105 https://dev.workflowhub.eu/workflows/1105?version=2 gtn, galaxy, microbiome 2024-07-16 2024-10-07 2 2 21.0 dada2_makeSequenceTable, collection_element_identifiers, cat1, dada2_assignTaxonomyAddspecies, Add_a_column1, dada2_plotQualityProfile, dada2_dada, tp_head_tool, dada2_removeBimeraDenovo, dada2_seqCounts, dada2_filterAndTrim, tp_replace_in_line, __SORTLIST__, dada2_learnErrors, dada2_mergePairs, tp_replace_in_column, phyloseq_from_dada2, __UNZIP_COLLECTION__ Visualisation, Deposition, Analysis, Variant calling, DNA barcoding MIT Galaxy Training Network True False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial dev.WorkflowHub 1101 https://dev.workflowhub.eu/workflows/1101?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 38.0 mothur_screen_seqs, mothur_sub_sample, mothur_cluster, mothur_make_biom, newick_display, mothur_count_groups, mothur_classify_seqs, mothur_dist_shared, mothur_tree_shared, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_seq_error, mothur_unique_seqs, mothur_classify_otu, mothur_align_seqs, mothur_summary_seqs, mothur_venn, taxonomy_krona_chart, mothur_filter_seqs, mothur_remove_seqs, mothur_summary_single, mothur_cluster_split, mothur_count_seqs, mothur_make_shared, mothur_remove_groups, mothur_pre_cluster, mothur_get_groups, mothur_chimera_vsearch, mothur_heatmap_sim, mothur_rarefaction_single, mothur_make_contigs, mothur_dist_seqs, XY_Plot_1 Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +Identification of the micro-organisms in a beer using Nanopore sequencing dev.WorkflowHub 1097 https://dev.workflowhub.eu/workflows/1097?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 8.0 Filter1, kraken2, krakentools_kreport2krona, fastp, taxonomy_krona_chart, porechop, fastqc Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Taxonomic classification, Sequencing quality control, Aggregation MIT Galaxy Training Network True False +Taxonomic Profiling and Visualization of Metagenomic Data dev.WorkflowHub 1095 https://dev.workflowhub.eu/workflows/1095?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 10.0 kraken_biom, kraken2, krakentools_kreport2krona, interactive_tool_phinch, taxonomy_krona_chart, est_abundance, metaphlan, interactive_tool_pavian, __UNZIP_COLLECTION__ Visualisation, Statistical calculation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Aggregation MIT Galaxy Training Network True False +Workflow 3: Functional Information (quick) dev.WorkflowHub 1080 https://dev.workflowhub.eu/workflows/1080?version=1 gtn, galaxy, asaim, metagenomics 2024-06-25 2024-10-07 1 1 12.0 humann_regroup_table, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Grep1, humann_unpack_pathways, humann_split_stratified_table, Cut1, humann_renorm_table Species frequency estimation, Phylogenetic analysis, Taxonomic classification MIT Galaxy Training Network True False +Amplicon Tutorial dev.WorkflowHub 1070 https://dev.workflowhub.eu/workflows/1070?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 17.0 mothur_make_shared, mothur_classify_otu, mothur_make_group, mothur_screen_seqs, mothur_pre_cluster, mothur_summary_seqs, mothur_align_seqs, mothur_filter_seqs, mothur_make_biom, krona-text, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_classify_seqs, mothur_merge_files Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" dev.WorkflowHub 1067 https://dev.workflowhub.eu/workflows/1067?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 7.0 humann2_renorm_table, taxonomy_krona_chart, humann2_regroup_table, metaphlan2, metaphlan2krona, humann2 Visualisation CC-BY-4.0 Galaxy Training Network True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads dev.WorkflowHub 1064 https://dev.workflowhub.eu/workflows/1064?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 11.0 kraken2, fastp, multiqc, tp_replace_in_line, porechop, taxonomy_krona_chart, Remove beginning1, fastqc, datamash_reverse Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Validation, Sequencing quality control, Taxonomic classification CC-BY-4.0 Galaxy Training Network True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] dev.WorkflowHub 1060 https://dev.workflowhub.eu/workflows/1060?version=1 gtn, galaxy, microbiome 2024-06-25 2024-10-07 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification MIT Galaxy Training Network True False +Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2024-12-20 2 2 collapse_dataset, humann, fastq_paired_end_interlacer, humann_unpack_pathways, collection_column_join, est_abundance, metaphlan, add_line_to_file, humann_regroup_table, bowtie2, collection_element_identifiers, humann_rename_table, sort1, krakentools_kreport2krona, csv_to_tabular, tp_easyjoin_tool, __UNZIP_COLLECTION__, krakentools_alpha_diversity, cat1, kraken2, taxpasta, tp_replace_in_line, taxonomy_krona_chart, __ZIP_COLLECTION__, datamash_transpose, fastp, Remove beginning1, tp_sed_tool, tp_text_file_with_recurring_lines, tp_awk_tool, humann_renorm_table Sequence contamination filtering, Statistical calculation, Nucleic acid sequence analysis, Visualisation, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Formatting, Aggregation, Standardisation and normalisation, Species frequency estimation, Conversion, Read mapping, Taxonomic classification MIT True False +ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 humann2_renorm_table, combine_metaphlan2_humann2, Grep1, fastq_paired_end_interlacer, metaphlan2krona, fastqc, humann2, multiqc, metaphlan2, group_humann2_uniref_abundances_to_go, humann2_genefamilies_genus_level, tp_sort_header_tool, cutadapt, export2graphlan, bg_sortmerna, taxonomy_krona_chart, humann2_unpack_pathways, graphlan_annotate, graphlan, Grouping1, format_metaphlan2_output Visualisation, Primer removal, Sequencing quality control, Formatting, Sequence similarity search, Conversion, Phylogenetic inference, Sequence trimming, Statistical calculation, Sequence comparison, Phylogenetic tree editing, Sequence composition calculation, Read pre-processing, Sequence alignment analysis, Validation, Phylogenetic tree visualisation, Taxonomic classification MIT True False +MAGs building with individual assembly https://usegalaxy.eu 0563f58718be932d https://usegalaxy.eu/published/workflow?id=0563f58718be932d Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler name:fairymags, name:microgalaxy 2024-12-20 2024-12-20 1 1 fastq_paired_end_joiner, checkm_plot, checkm_lineage_wf, collection_column_join, concoct_cut_up_fasta, bowtie2, drep_dereplicate, samtools_sort, multiqc, concoct_merge_cut_up_clustering, gtdbtk_classify_wf, semibin, quast, __FLATTEN__, __UNZIP_COLLECTION__, concoct_extract_fasta_bins, metabat2, megahit, concoct, metabat2_jgi_summarize_bam_contig_depths, Fasta_to_Contig2Bin, coverm_genome, das_tool, maxbin2, concoct_coverage_table Genome annotation, Read binning, Visualisation, Genome comparison, Sequence assembly, Sequencing quality control, Sequence assembly validation, Genome alignment, Read mapping, Statistical calculation, Sequence clustering, Genome assembly, Local alignment, Query and retrieval, Sequence composition calculation, Validation, Taxonomic classification MIT True False +MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 kallisto_quant, bg_sortmerna, trim_galore, collection_column_join, fastqc, __UNZIP_COLLECTION__ Statistical calculation, Primer removal, Sequencing quality control, Sequence comparison, Sequence similarity search, Read pre-processing, Sequence composition calculation, Sequence alignment analysis, Sequence trimming, Gene expression profiling MIT True False +MGnify's amplicon pipeline v5.0 https://usegalaxy.eu 02f90a96d01fed4f https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2024-05-06 2024-12-16 103 103 __MERGE_COLLECTION__, fastq_dl, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, tp_awk_tool Apache-2.0 True False +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 regexColumn1, cat1, Filter1, Add_a_column1, rbc_mafft, collapse_dataset, tab2fasta, bg_diamond_view, rapidnj, bg_diamond, gops_intersect_1, join1, Cut1, tp_split_on_column Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment True False +MGnify's amplicon pipeline v5.0 - Quality control SE https://usegalaxy.eu b7166aff73e5d81c https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-03-25 2024-11-26 16 16 fastq_filter, fastq_to_fasta_python, trimmomatic, tp_find_and_replace, prinseq, multiqc, cshl_fasta_formatter, fastqc Sequence contamination filtering, Read pre-processing, Sequence composition calculation, Statistical calculation, Sequence trimming, Validation, Sequencing quality control Apache-2.0 True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 featurecounts, multiqc, __FILTER_FAILED_DATASETS__, umi_tools_extract, collection_column_join, fastqc, rna_star Sequence composition calculation, Statistical calculation, Validation, Sequence alignment, RNA-Seq quantification, Read summarisation, Sequencing quality control MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 sqlite_to_tabular, unipept, search_gui, query_tabular, peptide_shaker Visualisation, Prediction and recognition MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 __EXTRACT_DATASET__, __BUILD_LIST__, Grep1, map_param_value, __FILTER_EMPTY_DATASETS__ MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 msconvert, Filter1, regex1, query_tabular, unipept, tp_replace_in_line, search_gui, Remove beginning1, tp_replace_in_column, flashlfq, Cut1, peptide_shaker Visualisation, Prediction and recognition, Filtering, Formatting, Label-free quantification MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_expand, metaquantome_stat, metaquantome_sample, metaquantome_filter, metaquantome_viz, metaquantome_db Visualisation, Indexing, Differential protein expression analysis, Statistical inference, Functional clustering, Query and retrieval, Quantification, Principal component visualisation, Heat map generation, Filtering MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 ampvis2_heatmap, ampvis2_ordinate, unzip, kraken2, trimmomatic, krakentools_kreport2krona, multiqc, taxonomy_krona_chart, ampvis2_load, collection_column_join, __FLATTEN__, fastqc, tp_cut_tool, cutadapt, lotus2 Visualisation, Statistical calculation, Analysis, Primer removal, Sequencing quality control, DNA barcoding, Aggregation, Sequence composition calculation, Read pre-processing, Sequence trimming, Validation, Sequence feature detection, Taxonomic classification MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, fastq_to_tabular, filter_tabular, recentrifuge, kraken2, seq_filter_by_id Expression analysis, Read mapping, Cross-assembly, Taxonomic classification MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 bowtie2, multiqc, featurecounts RNA-Seq quantification, Validation, Sequencing quality control, Read mapping, Read summarisation MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control MIT True False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.eu 64abcddeb516a712 https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 - Quality control PE https://usegalaxy.eu f9648091c06171cd https://usegalaxy.eu/published/workflow?id=f9648091c06171cd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-27 2024-10-25 16 16 fastq_filter, fastq_to_fasta_python, trimmomatic, tp_find_and_replace, prinseq, mgnify_seqprep, fastp, multiqc, cshl_fasta_formatter, fastqc, __UNZIP_COLLECTION__ Sequence contamination filtering, Statistical calculation, Sequencing quality control, Nucleic acid design, Read pre-processing, Sequence composition calculation, Sequence trimming, Validation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - rRNA prediction https://usegalaxy.eu 0c3eee883f5ab977 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2024-05-06 2024-10-25 31 31 collection_element_identifiers, gops_concat_1, infernal_cmsearch, taxonomy_krona_chart, cmsearch_deoverlap, cshl_fasta_formatter, __FILTER_EMPTY_DATASETS__, biom_convert, mapseq, query_tabular, bedtools_getfastabed, __FILTER_FROM_FILE__, tp_awk_tool k-mer counting, Mapping, Visualisation, Alignment, Nucleic acid feature detection, Formatting, Comparison Apache-2.0 True False +Taxonomic abundance summary tables for a specified taxonomic rank https://usegalaxy.eu b57fa7ac24a1e777 https://usegalaxy.eu/published/workflow?id=b57fa7ac24a1e777 Rand Zoabi mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-09-27 2024-10-25 1 1 filter_tabular, map_param_value, Grouping1, collection_column_join, tp_awk_tool MIT True False +MGnify's amplicon pipeline v5.0 - ITS https://usegalaxy.eu 169327ba670607d1 https://usegalaxy.eu/published/workflow?id=169327ba670607d1 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-06 2024-10-25 24 24 collection_element_identifiers, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, bedtools_maskfastabed, biom_convert, mapseq, __FILTER_FROM_FILE__, tp_awk_tool k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False +MGnify amplicon summary tables https://usegalaxy.eu 05dc8f4321a42cdc https://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdc Rand Zoabi mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2024-05-22 2024-10-25 69 69 filter_tabular, collection_column_join, Grouping1, query_tabular, tp_awk_tool MIT True False +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2024-09-19 1 1 regexColumn1, krakentools_extract_kraken_reads, Add_a_column1, kraken2, samtools_fastx, collapse_dataset, multiqc, fastp, nanoplot, porechop, Grep1, __FILTER_FAILED_DATASETS__, collection_column_join, fastqc, bamtools_split_mapped, minimap2, Cut1 Sequence contamination filtering, Visualisation, Statistical calculation, Scatter plot plotting, Sequencing quality control, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, Sequence composition calculation, Sequence alignment analysis, Validation, Data handling, Taxonomic classification MIT False False +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.eu 77e5bbd317750915 https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +Allele-based Pathogen Identification (release v0.1) https://usegalaxy.eu d215a2e554fd83bc https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.eu cdf2f02428f5f83f https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microgalaxy, name:wgs 2024-07-16 2024-07-28 16 16 regexColumn1, bowtie2, ggplot2_heatmap, freebayes, trimmomatic, bcftools_norm, abricate, multiqc, bcftools_view, Remove beginning1, vcf2tsv, Grouping1, collection_column_join, __FLATTEN__, fastqc, snpSift_filter, tp_awk_tool, shovill Visualisation, Statistical calculation, Genome assembly, Sequencing quality control, Sequence composition calculation, Variant calling, Validation, Read mapping, Antimicrobial resistance prediction MIT False False +MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microgalaxy 2023-11-15 2024-07-11 14 14 fastq_paired_end_interlacer, checkm_lineage_wf, concoct_cut_up_fasta, bowtie2, drep_dereplicate, samtools_sort, concoct_merge_cut_up_clustering, semibin, quast, __UNZIP_COLLECTION__, concoct_extract_fasta_bins, metabat2, megahit, concoct, metabat2_jgi_summarize_bam_contig_depths, Fasta_to_Contig2Bin, coverm_genome, das_tool, maxbin2, concoct_coverage_table Genome annotation, Statistical calculation, Read binning, Sequence clustering, Visualisation, Genome comparison, Sequence assembly, Genome assembly, Sequencing quality control, Local alignment, Sequence composition calculation, Sequence assembly validation, Validation, Read mapping False False +PathoGFAIR https://usegalaxy.eu 0dce37adb369492c https://usegalaxy.eu/published/workflow?id=0dce37adb369492c Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-05-31 2024-07-03 93 93 MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-04-03 2024-06-24 58 58 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-04-12 2024-06-24 72 72 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2023-04-12 2024-06-24 190 190 regexColumn1, krakentools_extract_kraken_reads, Add_a_column1, kraken2, samtools_fastx, collapse_dataset, multiqc, fastp, nanoplot, porechop, Grep1, __FILTER_FAILED_DATASETS__, collection_column_join, fastqc, bamtools_split_mapped, minimap2, Cut1 Sequence contamination filtering, Visualisation, Statistical calculation, Scatter plot plotting, Sequencing quality control, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, Sequence composition calculation, Sequence alignment analysis, Validation, Data handling, Taxonomic classification MIT False False +Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:gtn 2023-04-12 2024-06-19 8 8 interactive_tool_phinch, kraken_biom, kraken2 Taxonomic classification MIT False False +metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microgalaxy 2023-12-14 2024-06-19 0 0 msconvert, Filter1, regex1, query_tabular, unipept, tp_replace_in_line, search_gui, Remove beginning1, tp_replace_in_column, flashlfq, Cut1, peptide_shaker Visualisation, Prediction and recognition, Filtering, Formatting, Label-free quantification False False +Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2023-04-13 2024-06-05 142 142 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-05-11 2024-06-05 58 58 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, iwc, name:collection, name:microgalaxy 2022-11-29 2024-04-04 205 205 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, interactive_tool_jupyter_notebook, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microgalaxy 2023-10-10 2024-03-15 128 128 interactive_tool_jupyter_notebook, __BUILD_LIST__ True False +Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microgalaxy 2023-09-25 2024-03-13 80 80 __EXTRACT_DATASET__, __BUILD_LIST__, Grep1, map_param_value, __FILTER_EMPTY_DATASETS__ False False +WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences Target-Decoy, Protein identification, de Novo sequencing, Expression analysis, Tag-based peptide identification False False +WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 msconvert, filter_tabular, Filter1, query_tabular, Cut1, fasta2tab, tp_cat, Grep1, search_gui, ident_params, Remove beginning1, Grouping1, fasta_cli, fasta_merge_files_and_filter_unique_sequences, dbbuilder, maxquant, peptide_shaker Visualisation, Statistical calculation, Formatting, Clustering, Standardisation and normalisation, Principal component plotting, Protein quantification, Imputation, Heat map generation, Filtering False False +WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 uniprotxml_downloader, Filter1, collapse_dataset, query_tabular, Cut1, pepquery2, tp_cat, Remove beginning1, Grouping1, fasta_merge_files_and_filter_unique_sequences, dbbuilder False False +WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 Grep1, Cut1, Grouping1, maxquant Visualisation, Statistical calculation, Clustering, Standardisation and normalisation, Principal component plotting, Protein quantification, Imputation, Heat map generation False False +WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 Grep1, unipept, msstatstmt Visualisation, Prediction and recognition False False +MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 fraggenescan, sort1, kofamscan, coverm_contig, cat_bins, trim_galore, coverm_genome, tp_cat, fasplit, checkm_lineage_wf, hmmer_hmmscan, quast, fastqc, interproscan, maxbin2, tp_grep_tool, tp_awk_tool Visualisation, Sequence motif recognition, Gene functional annotation, Sequence assembly, Database search, Primer removal, Sequencing quality control, Format validation, Formatting, Multiple sequence alignment, Coding region prediction, Conversion, Sequence analysis, Sequence database search, Sequence trimming, Sequence assembly validation, Sequence profile generation, Probabilistic sequence generation, Protein feature detection, Gene prediction, Statistical calculation, Local alignment, Read pre-processing, Sequence composition calculation, Sequence generation, Data retrieval, Validation, Taxonomic classification False False +MetaP https://usegalaxy.eu 01ac8bf9832789e2 https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 name:microgalaxy 2023-12-14 2023-12-14 1 1 maxquant Visualisation, Statistical calculation, Clustering, Standardisation and normalisation, Principal component plotting, Protein quantification, Imputation, Heat map generation False False +MetaT https://usegalaxy.eu 3733bcdf5b458be7 https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 name:microgalaxy 2023-12-14 2023-12-14 1 1 kallisto_quant, bg_sortmerna, trim_galore, collection_column_join, fastqc, __UNZIP_COLLECTION__ Statistical calculation, Primer removal, Sequencing quality control, Sequence comparison, Sequence similarity search, Read pre-processing, Sequence composition calculation, Sequence alignment analysis, Sequence trimming, Gene expression profiling False False +metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_expand, metaquantome_stat, metaquantome_sample, metaquantome_filter, metaquantome_viz, metaquantome_db Visualisation, Indexing, Differential protein expression analysis, Statistical inference, Functional clustering, Query and retrieval, Quantification, Principal component visualisation, Heat map generation, Filtering False False +metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_expand, metaquantome_stat, metaquantome_sample, metaquantome_filter, metaquantome_viz, metaquantome_db Visualisation, Indexing, Differential protein expression analysis, Statistical inference, Functional clustering, Query and retrieval, Quantification, Principal component visualisation, Heat map generation, Filtering False False +Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 sqlite_to_tabular, unipept, search_gui, query_tabular, peptide_shaker Visualisation, Prediction and recognition False False +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 collapse_dataset, Cut1, tp_cat, Grep1, random_lines1, join1, tp_grep_tool, Filter1, bedtools_complementbed, tp_sort_header_tool, addValue, fasta_compute_length, cat1, lastz_wrapper_2, bedtools_sortbed, fasta_filter_by_length, mergeCols1, bedtools_intersectbed, tp_sed_tool, datamash_ops Sequence alignment, Read mapping, Mapping True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken2, fastp, multiqc, tp_replace_in_line, porechop, taxonomy_krona_chart, Remove beginning1, fastqc, datamash_reverse Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Validation, Sequencing quality control, Taxonomic classification False False +Main Metatranscriptomics Analysis https://usegalaxy.eu 7a08ecdf23e0c7a3 https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep name:microgalaxy 2023-12-14 2023-12-14 0 0 MIT False False +Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 miniasm, racon, PlasFlow, nanoplot, gfa_to_fa, bandage_image, unicycler, minimap2, staramr_search Genome assembly, Scatter plot plotting, Sequence assembly visualisation, Mapping assembly, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, De-novo assembly, Sequence analysis False False +Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 Filter1, kraken2, krakentools_kreport2krona, fastp, taxonomy_krona_chart, porechop, fastqc Sequence contamination filtering, Sequence composition calculation, Visualisation, Statistical calculation, Taxonomic classification, Sequencing quality control, Aggregation MIT False False +workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microgalaxy 2023-12-14 2023-12-14 0 0 bowtie2, filter_tabular, ngsutils_bam_filter, megahit, tp_cat, seqtk_subseq, random_lines1, bamtools, fastqc, cutadapt, bg_uniq Sequence contamination filtering, Statistical calculation, Genome assembly, Primer removal, Sequencing quality control, Sequence file editing, Formatting, Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence alignment analysis, Variant calling, Read mapping, Data handling False False +Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microgalaxy 2023-12-14 2023-12-14 0 0 bowtie2, bandage_info, megahit_contig2fastg, megahit, bandage_image, collection_column_join, quast, metaspades Visualisation, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Read mapping False False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 humann2_renorm_table, taxonomy_krona_chart, humann2_regroup_table, metaphlan2, metaphlan2krona, humann2 Visualisation False False +Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken_biom, kraken2, krakentools_kreport2krona, interactive_tool_phinch, taxonomy_krona_chart, est_abundance, metaphlan, interactive_tool_pavian, __UNZIP_COLLECTION__ Visualisation, Statistical calculation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Aggregation MIT False False +Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_make_shared, mothur_classify_otu, mothur_make_group, mothur_screen_seqs, mothur_pre_cluster, mothur_summary_seqs, mothur_align_seqs, mothur_filter_seqs, mothur_make_biom, krona-text, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_classify_seqs, mothur_merge_files Visualisation, Sequence clustering, DNA barcoding, Sequencing quality control, Phylogenetic analysis, Sequence read processing, Taxonomic classification False False +Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, jbrowse Phylogenetic tree visualisation, Phylogenetic tree generation, Genome visualisation, Variant calling False False +Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 freebayes, picard_MergeSamFiles, vcffilter2, vcf2tsv, bwa_mem, fastqc, bamFilter, Cut1, bamleftalign, picard_MarkDuplicates Statistical calculation, Sequence alignment, Sequencing quality control, Formatting, Generation, Genome indexing, Sequence composition calculation, Sequence alignment analysis, Variant calling, Read mapping, Data handling False False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_screen_seqs, mothur_sub_sample, mothur_cluster, mothur_make_biom, newick_display, mothur_count_groups, mothur_classify_seqs, mothur_dist_shared, mothur_tree_shared, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_seq_error, mothur_unique_seqs, mothur_classify_otu, mothur_summary_seqs, mothur_align_seqs, mothur_venn, taxonomy_krona_chart, mothur_filter_seqs, mothur_remove_seqs, mothur_summary_single, mothur_cluster_split, mothur_count_seqs, mothur_make_shared, mothur_remove_groups, mothur_pre_cluster, mothur_get_groups, mothur_chimera_vsearch, mothur_heatmap_sim, mothur_rarefaction_single, mothur_make_contigs, mothur_dist_seqs, XY_Plot_1 Visualisation, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Sequence read processing, Taxonomic classification False False +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 regexColumn1, cat1, Filter1, Add_a_column1, rbc_mafft, collapse_dataset, tab2fasta, bg_diamond_view, rapidnj, bg_diamond, gops_intersect_1, join1, Cut1, tp_split_on_column Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment True False +Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 prokka, fastqc, multiqc, quast, unicycler Gene prediction, Genome annotation, Statistical calculation, Visualisation, Genome assembly, Sequencing quality control, Aggregation, Coding region prediction, Sequence composition calculation, Sequence assembly validation, Validation False False +Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 list_organism, iframe, create_account, create_or_update, jbrowse Genome visualisation True False +Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 prokka, jbrowse Gene prediction, Coding region prediction, Genome visualisation, Genome annotation False False +Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 trimmomatic, ncbi_blastn_wrapper, regex_replace, deeptools_bam_coverage, tp_cat, fasta2tab, Grep1, join1, bg_column_arrange_by_header, medaka_consensus_pipeline, circos_interval_to_tile, staramr_search, prokka, Filter1, Add_a_column1, regex1, nanoplot, tp_sort_header_tool, gff2bed1, tp_easyjoin_tool, circos_gc_skew, fasta_compute_length, flye, tp_head_tool, bandage_image, minimap2, tbl2gff3, tab2fasta, PlasFlow, jbrowse, circos_wiggle_to_scatter, tp_text_file_with_recurring_lines, circos, tp_cut_tool, Cut1, tp_split_on_column Gene prediction, Genome annotation, Genome assembly, Scatter plot plotting, Sequence assembly, Mapping assembly, Sequence assembly visualisation, Base-calling, Box-Whisker plot plotting, Sequence visualisation, Cross-assembly, Coding region prediction, De-novo assembly, Pairwise sequence alignment, Sequence analysis, Variant calling, Genome visualisation True False +Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 raxml, interactive_tool_rstudio Phylogenetic tree analysis, Sequence analysis False False +From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 bcftools_consensus, snp_sites, tp_cat, tb_variant_filter, snp_dists True False +From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, tb_variant_filter, __MERGE_COLLECTION__, trimmomatic Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling True False +From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 addName, __MERGE_COLLECTION__, tp_replace_in_line, tp_cat, tp_sed_tool, tp_grep_tool, samtools_view, tb_profiler_profile Antimicrobial resistance prediction True False +M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken2, trimmomatic, multiqc, tb_variant_filter, tbvcfreport, fastqc, snippy, jbrowse, tb_profiler_profile Statistical calculation, Phylogenetic tree generation, Sequencing quality control, Sequence composition calculation, Variant calling, Validation, Phylogenetic tree visualisation, Genome visualisation, Antimicrobial resistance prediction, Taxonomic classification MIT False False +Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bowtie2, freebayes, bcftools_norm, bcftools_view, vcf2tsv, snpSift_filter, tp_awk_tool Variant calling, Read mapping, Statistical calculation True False +Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bowtie2, collection_element_identifiers, freebayes, bcftools_norm, collapse_dataset, tp_cat, samtools_coverage, samtools_depth, vcf2tsv Variant calling, Read mapping, Statistical calculation True False +MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 mgnify_amplicon_showcase, name:microgalaxy 2023-12-12 2023-12-13 1 1 gops_concat_1, infernal_cmsearch, taxonomy_krona_chart, cmsearch_deoverlap, bedtools_maskfastabed, biom_convert, mapseq, query_tabular, bedtools_getfastabed, tp_awk_tool Mapping, k-mer counting, Visualisation, Alignment, Nucleic acid feature detection, Formatting, Comparison False False +MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 mgnify_amplicon_showcase, name:microgalaxy 2023-12-13 2023-12-13 1 1 fastq_to_fasta_python, trimmomatic, tp_find_and_replace, prinseq, fastp, multiqc, cshl_fasta_formatter, iuc_pear, fastqc, fastq_dump, __UNZIP_COLLECTION__ Sequence contamination filtering, Statistical calculation, Sequencing quality control, Read pre-processing, Sequence composition calculation, Sequence trimming, Validation, Data handling, Sequence merging False False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-10 2023-12-07 2 2 bowtie2, multiqc, featurecounts RNA-Seq quantification, Validation, Sequencing quality control, Read mapping, Read summarisation False False +Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 72 72 bowtie2, cat1, metaeuk_easy_predict, multiqc, megahit, translate_nucleotides, bg_diamond, eggnog_mapper, kofamscan, quast, fastqc, bedtools_getfastabed, dbbuilder, metagene_annotator, bg_diamond_makedb, cd_hit Genome annotation, Homology-based gene prediction, Information extraction, Visualisation, Gene functional annotation, Sequencing quality control, Fold recognition, Sequence analysis, Sequence assembly validation, Read mapping, Mapping, Statistical calculation, Sequence clustering, Genome assembly, Query and retrieval, Sequence composition calculation, Sequence alignment analysis, Validation, Sequence annotation False False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 51 51 trimmomatic, multiqc, fastqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control False False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microgalaxy 2022-06-29 2023-12-07 28 28 bowtie2, fastq_to_tabular, filter_tabular, recentrifuge, kraken2, seq_filter_by_id Expression analysis, Read mapping, Cross-assembly, Taxonomic classification False False +Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microgalaxy 2022-09-03 2023-12-07 18 18 maaslin2, kraken_biom, recentrifuge, kraken2, interactive_tool_phinch Standardisation and normalisation, Statistical calculation, Visualisation, Expression analysis, Filtering, Cross-assembly, Taxonomic classification False False +pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:functionalprofiling 2023-07-07 2023-07-07 3 3 humann_regroup_table, humann_rename_table, humann, tp_find_and_replace, combine_metaphlan2_humann2, Grep1, humann_unpack_pathways, humann_split_stratified_table, Cut1, humann_renorm_table Species frequency estimation, Phylogenetic analysis, Taxonomic classification MIT False False + pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:communityprofiling 2023-06-30 2023-07-06 3 3 export2graphlan, graphlan_annotate, taxonomy_krona_chart, graphlan, metaphlan, Cut1 Visualisation, Nucleic acid sequence analysis, Phylogenetic tree editing, Phylogenetic tree analysis, Conversion, Phylogenetic inference, Phylogenetic tree visualisation, Taxonomic classification MIT False False + pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:adaptedasiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2023-07-06 2 2 bg_sortmerna, multiqc, fastq_paired_end_interlacer, __FLATTEN__, fastqc, cutadapt Statistical calculation, Primer removal, Sequencing quality control, Sequence comparison, Sequence similarity search, Sequence composition calculation, Read pre-processing, Sequence alignment analysis, Sequence trimming, Validation MIT False False +MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Visualisation, Statistical calculation, Clustering, Standardisation and normalisation, Principal component plotting, Protein quantification, Imputation, Heat map generation False False +MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 fraggenescan, sort1, kofamscan, coverm_contig, cat_bins, trim_galore, coverm_genome, tp_cat, fasplit, checkm_lineage_wf, hmmer_hmmscan, quast, fastqc, interproscan, maxbin2, tp_grep_tool, tp_awk_tool Visualisation, Sequence motif recognition, Gene functional annotation, Sequence assembly, Database search, Primer removal, Sequencing quality control, Format validation, Formatting, Multiple sequence alignment, Coding region prediction, Conversion, Sequence analysis, Sequence database search, Sequence trimming, Sequence assembly validation, Sequence profile generation, Probabilistic sequence generation, Protein feature detection, Gene prediction, Statistical calculation, Local alignment, Read pre-processing, Sequence composition calculation, Sequence generation, Data retrieval, Validation, Taxonomic classification False False +MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 kallisto_quant, bg_sortmerna, trim_galore, collection_column_join, fastqc, __UNZIP_COLLECTION__ Statistical calculation, Primer removal, Sequencing quality control, Sequence comparison, Sequence similarity search, Read pre-processing, Sequence composition calculation, Sequence alignment analysis, Sequence trimming, Gene expression profiling False False +Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.org 29ba77708cdafe0f https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-11-28 2024-11-28 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org 6d778eeb176d563c https://usegalaxy.org/published/workflow?id=6d778eeb176d563c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org 4b5f6b5d4f36e38b https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org 3ef08553982f6ffc https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org 3f252e077e0bcce5 https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org 2d3063882d8239ff https://usegalaxy.org/published/workflow?id=2d3063882d8239ff Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +PathoGFAIR (imported from uploaded file) https://usegalaxy.org e55593af91337a05 https://usegalaxy.org/published/workflow?id=e55593af91337a05 Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-07-03 2024-07-03 0 0 MIT False False +Taxonomy Profiling and Visualization with Krona https://usegalaxy.org 8f5904693b5f74f4 https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Gene-based Pathogen Identification https://usegalaxy.org cce88bc57b180d09 https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +Allele-based Pathogen Identification https://usegalaxy.org 38911ba6f66d80f6 https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Nanopore Preprocessing https://usegalaxy.org 574e42683dc3961b https://usegalaxy.org/published/workflow?id=574e42683dc3961b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 regexColumn1, krakentools_extract_kraken_reads, Add_a_column1, kraken2, samtools_fastx, collapse_dataset, multiqc, fastp, nanoplot, porechop, Grep1, __FILTER_FAILED_DATASETS__, collection_column_join, fastqc, bamtools_split_mapped, minimap2, Cut1 Sequence contamination filtering, Visualisation, Statistical calculation, Scatter plot plotting, Sequencing quality control, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, Sequence composition calculation, Sequence alignment analysis, Validation, Data handling, Taxonomic classification MIT False False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org.au 857e482acfcb2dba https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org.au 131636a795bac485 https://usegalaxy.org.au/published/workflow?id=131636a795bac485 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org.au b60922a253df6654 https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Nanopore Preprocessing (release v0.1) https://usegalaxy.org.au 69d91340fc7effa2 https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2024-09-19 1 1 regexColumn1, krakentools_extract_kraken_reads, Add_a_column1, kraken2, samtools_fastx, collapse_dataset, multiqc, fastp, nanoplot, porechop, Grep1, __FILTER_FAILED_DATASETS__, collection_column_join, fastqc, bamtools_split_mapped, minimap2, Cut1 Sequence contamination filtering, Visualisation, Statistical calculation, Scatter plot plotting, Sequencing quality control, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, Sequence composition calculation, Sequence alignment analysis, Validation, Data handling, Taxonomic classification MIT False False +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org.au 084bb76cf47d7060 https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +PathoGFAIR (imported from uploaded file) https://usegalaxy.org.au f5f9808fb50b6f2c https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-07-03 2024-07-03 0 0 MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org.au eda40b58616a0fe4 https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 fasttree, collapse_dataset, fasta2tab, collection_column_join, newick_display, regexColumn1, ggplot2_heatmap, regex1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, clustalw, fasta_merge_files_and_filter_unique_sequences, bedtools_getfastabed, Count1, tp_replace_in_column, tp_sorted_uniq, tab2fasta, __FILTER_FAILED_DATASETS__, Remove beginning1, Grouping1, Cut1, tp_split_on_column Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation, Multiple sequence alignment, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Mapping, Phylogenetic tree reconstruction MIT False False +Allele-based Pathogen Identification https://usegalaxy.org.au 244ea5e94237ebad https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 bcftools_consensus, Paste1, regexColumn1, snpSift_extractFields, bcftools_norm, tp_head_tool, collapse_dataset, table_compute, samtools_depth, samtools_coverage, Remove beginning1, snpSift_filter, Count1, clair3, CONVERTER_gz_to_uncompressed, tp_cut_tool, minimap2, Cut1 Pairwise sequence alignment, Variant calling MIT False False +Gene-based Pathogen Identification https://usegalaxy.org.au ef8c22c2525063a2 https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 collection_element_identifiers, flye, param_value_from_file, tab2fasta, tp_find_and_replace, compose_text_param, abricate, __BUILD_LIST__, fasta2tab, split_file_to_collection, bandage_image, medaka_consensus_pipeline Genome assembly, Sequence assembly visualisation, Mapping assembly, Sequence assembly, Base-calling, Cross-assembly, De-novo assembly, Variant calling, Antimicrobial resistance prediction MIT False False +Taxonomy Profiling and Visualization with Krona https://usegalaxy.org.au d9ba165e6ae55417 https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 krakentools_kreport2krona, taxonomy_krona_chart, kraken2 Visualisation, Taxonomic classification, Aggregation MIT False False +Nanopore Preprocessing https://usegalaxy.org.au 25d52afddaa3451b https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 regexColumn1, krakentools_extract_kraken_reads, Add_a_column1, kraken2, samtools_fastx, collapse_dataset, multiqc, fastp, nanoplot, porechop, Grep1, __FILTER_FAILED_DATASETS__, collection_column_join, fastqc, bamtools_split_mapped, minimap2, Cut1 Sequence contamination filtering, Visualisation, Statistical calculation, Scatter plot plotting, Sequencing quality control, Box-Whisker plot plotting, Aggregation, Pairwise sequence alignment, Sequence composition calculation, Sequence alignment analysis, Validation, Data handling, Taxonomic classification MIT False False diff --git 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ExpandNameSourceIDLinkCreatorsTagsCreation timeUpdate timeLatest versionVersionsNumber of stepsToolsEDAM operationsEDAM topicsLicenseDOIProjects
Taxonomy classification using Kraken2 and BrackenWorkflowHub1199https://workflowhub.eu/workflows/1199?version=2Valentine Murigneux, Mike Thanggucfg2galaxy, metagenomics, name:collection, shotgun2024-12-102024-12-102229.0Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, kraken2, krakentools_beta_diversity, collection_element_identifiers, regex1, add_line_to_file, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, Prepare alpha diversity summary file\nPaste1, est_abundance, cat_multiple, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1, taxonomy_krona_chart, collection_column_join, krakentools_alpha_diversity, __RELABEL_FROM_FILE__, Extract column name and fraction_total_reads from Bracken report\nCut1, krakentools_kreport2krona, krakentools_combine_kreportsAggregation, Visualisation, Statistical calculation, Taxonomic classificationMetagenomics, TaxonomyCC-BY-4.010.48546/workflowhub.workflow.1199.2QCIF Bioinformatics
AMR-PathfinderWorkflowHub1189https://workflowhub.eu/workflows/1189?version=2Helena Rasche, Dennis Dollée, Birgit Rijversamr, amr-detection, benchamrking2024-11-142024-11-142236.0, staramr_search, hamronize_tool, abricate, tp_find_and_replace, __MERGE_COLLECTION__, datamash_ops, tp_text_file_with_recurring_lines, hamronize_summarize, tp_split_on_column, collapse_dataset, cat_multi_datasets, addValue, __APPLY_RULES__, cat1, Cut1, cast, shovill, Grep1Data handling, Antimicrobial resistance prediction, Genome assembly, ParsingMITSeq4AMR, ErasmusMC Clinical Bioinformatics
bacterial-genome-assembly/mainWorkflowHub1043https://workflowhub.eu/workflows/1043?version=7Abromics None, Pierre Marin, Clea Siguretabromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality2024-11-262024-11-26777.0refseq_masher_matches, tooldistillator_summarize, bandage_image, quast, shovill, tooldistillator, bandage_infoData handling, Sequence assembly validation, Parsing, Visualisation, Genome assembly, Sequence assembly visualisationGPL-3.0-or-laterIntergalactic Workflow Commission (IWC)
quality-and-contamination-control/mainWorkflowHub1052https://workflowhub.eu/workflows/1052?version=8ABRomics None, Pierre Marin, Clea Siguretabromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming2024-11-232024-11-23886.0tooldistillator_summarize, kraken2, est_abundance, fastp, tooldistillator, recentrifugeData handling, Expression analysis, Sequencing quality control, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Cross-assembly, ParsingGPL-3.0-or-laterIntergalactic Workflow Commission (IWC)
Workflow 4: StaramrWorkflowHub470https://workflowhub.eu/workflows/470?version=110.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance2023-05-112024-09-091110.0hamronize_tool, abricate, collapse_dataset, tp_find_and_replace, shovill, hamronize_summarize, staramr_searchData handling, Antimicrobial resistance prediction, Genome assembly, ParsingGPL-3.0Seq4AMR
bacterial_genome_annotation/mainWorkflowHub1050https://workflowhub.eu/workflows/1050?version=9ABRomics None, Pierre Marin, Clea Siguretabromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation2024-10-262024-10-26996.0tooldistillator_summarize, bakta, integron_finder, plasmidfinder, isescan, tooldistillatorProtein feature detection, Data handling, Nucleic acid feature detection, Multilocus sequence typing, Genome annotation, Sequence motif recognition, Scaffolding, Structural variation detection, Genome assembly, ParsingGPL-3.0-or-laterIntergalactic Workflow Commission (IWC)
amr_gene_detection/mainWorkflowHub1049https://workflowhub.eu/workflows/1049?version=7ABRomics None, Pierre Marin, Clea Siguretabromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta2024-10-262024-10-27775.0abricate, tooldistillator_summarize, staramr_search, amrfinderplus, tooldistillatorData handling, Antimicrobial resistance prediction, ParsingGPL-3.0-or-laterIntergalactic Workflow Commission (IWC)
Analyses of shotgun metagenomics data with MetaPhlAn2WorkflowHub624https://workflowhub.eu/workflows/624?version=1Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batutgucfg2galaxy, metagenomics, shotgun2023-10-262024-04-051117.0, metaphlan2krona, metaphlan2, Cut1, taxonomy_krona_chart, humann2_renorm_table, humann2, humann2_regroup_table, merge_metaphlan_tablesPhylogenetic tree analysis, Nucleic acid sequence analysis, VisualisationMetagenomic sequencing, MetagenomicsCC-BY-4.010.48546/workflowhub.workflow.624.1QCIF Bioinformatics
Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]WorkflowHub653https://workflowhub.eu/workflows/653?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09114.0mothur_tree_shared, mothur_dist_shared, mothur_heatmap_sim, newick_displayTaxonomic classification, Phylogenetic tree analysis, Sequencing quality control, Phylogenetic analysis, Phylogenetic tree generation, Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]WorkflowHub652https://workflowhub.eu/workflows/652?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09113.0mothur_rarefaction_single, XY_Plot_1, mothur_summary_singleTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]WorkflowHub651https://workflowhub.eu/workflows/651?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09115.0mothur_make_shared, mothur_cluster_split, mothur_sub_sample, mothur_classify_otu, mothur_count_groupsTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]WorkflowHub650https://workflowhub.eu/workflows/650?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09112.0mothur_remove_lineage, mothur_classify_seqsTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]WorkflowHub648https://workflowhub.eu/workflows/648?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09115.0mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_screen_seqsTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]WorkflowHub649https://workflowhub.eu/workflows/649?version=1Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdimetagenomics2023-11-092023-11-09119.0mothur_pre_cluster, mothur_screen_seqs, mothur_remove_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_summary_seqsTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcodingCC-BY-4.0QCIF Bioinformatics
pox-virus-amplicon/mainWorkflowHub439https://workflowhub.eu/workflows/439?version=2Viktoria Isabel Schwarz, Wolfgang Maiervirology, pox2024-06-222024-06-222240.0\n Cut1, samtools_view, fastp, \n __SORTLIST__, samtools_merge, ivar_consensus, split_file_to_collection, \n __ZIP_COLLECTION__, \n __APPLY_RULES__, \n Grep1, tp_sed_tool, EMBOSS: maskseq51, datamash_ops, samtools_stats, \n param_value_from_file, \n __FILTER_FAILED_DATASETS__, compose_text_param, qualimap_bamqc, fasta_compute_length, ivar_trim, bwa_mem, \n __FLATTEN__, collection_element_identifiers, multiqc, tp_catSequence alignment analysis, Read mapping, Sequencing quality control, Local alignment, Sequence alignment, Genome indexing, Sequence contamination filtering, Global alignment, Sequence analysis, Generation, ValidationMITIntergalactic Workflow Commission (IWC)
3: Plant virus explorationWorkflowHub103https://workflowhub.eu/workflows/103?version=1de_novo, virology, exploration2021-02-042023-02-13112.0fastp, shovillSequencing quality control, Sequence contamination filtering, Genome assemblyApache-2.0Integrated and Urban Plant Pathology Laboratory
2: Plant virus confirmationWorkflowHub102https://workflowhub.eu/workflows/102?version=1assembly, virology, blast, mapping, reads_selection2021-02-042023-02-13117.0fasta_merge_files_and_filter_unique_sequences, minimap2, samtools_stats, ngsutils_bam_filter, shovill, picard_SamToFastq, ncbi_blastn_wrapperVariant calling, Sequence contamination filtering, Read pre-processing, Genome assembly, Sequencing quality control, Pairwise sequence alignment, FormattingApache-2.0Integrated and Urban Plant Pathology Laboratory
GTN Training - Antibiotic Resistance DetectionWorkflowHub406https://workflowhub.eu/workflows/406?version=1Saskia Hiltemann, Willem de Koningmetagenomics2022-11-242023-02-131112.0gfa_to_fa, bandage_image, nanoplot, staramr_search, minimap2, PlasFlow, miniasm, racon, unicyclerAggregation, Scatter plot plotting, De-novo assembly, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Sequence analysis, Genome assembly, Mapping assemblyMicrobiologyCC-BY-4.0Galaxy Training Network
1: Plant virus detection with kraken2 (SE)WorkflowHub124https://workflowhub.eu/workflows/124?version=1virology, kraken2021-06-172023-02-13113.0taxonomy_krona_chart, Kraken2Tax, kraken2Visualisation, Taxonomic classificationApache-2.0Integrated and Urban Plant Pathology Laboratory
1: Plant virus detection with kraken2 (PE)WorkflowHub101https://workflowhub.eu/workflows/101?version=1virology, kraken2021-02-042023-02-13113.0taxonomy_krona_chart, Kraken2Tax, kraken2Visualisation, Taxonomic classificationApache-2.0Integrated and Urban Plant Pathology Laboratory
Halophiles workup of Comparative gene analysishttps://usegalaxy.eua2c46deea34d9d80https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80Anton Nekrutenkogenome-annotation, name:microgalaxy2024-12-032024-12-0522cat1, tp_split_on_column, Add_a_column1, regexColumn1, collapse_dataset, join1, Cut1, tab2fasta, rapidnj, rbc_mafft, bg_diamond, bg_diamond_view, Filter1, gops_intersect_1Multiple sequence alignment, Sequence alignment analysis, Phylogenetic tree generation
pAllori Blood RNAhttps://usegalaxy.euca9d3233b0912765https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765Engy Nasr, Paul Zierepname:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics2023-07-022024-11-244343fastqc, __FILTER_FAILED_DATASETS__, rna_star, featurecounts, multiqc, collection_column_join, umi_tools_extractRead summarisation, Statistical calculation, Sequence composition calculation, Sequencing quality control, Sequence alignment, Validation, RNA-Seq quantificationMIT
Metaproteomics workflowhttps://usegalaxy.eucefc49c13ff73231https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehtaname:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy2024-11-212024-11-214040search_gui, peptide_shaker, unipept, query_tabular, sqlite_to_tabularVisualisation, Prediction and recognitionMIT
Feature-Count Table Normalizationhttps://usegalaxy.eu6239178d7cc4ac68https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68Johannes Effenbergername:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle2024-11-212024-11-2155__EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__, map_param_value, __BUILD_LIST__, Grep1MIT
metaQuantome_datacreation_workflowhttps://usegalaxy.eucd675ab32d3e7833https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Craneproteomics, name:microgalaxy2024-11-212024-11-2111msconvert, search_gui, peptide_shaker, Cut1, regex1, unipept, tp_replace_in_line, Remove beginning1, query_tabular, flashlfq, Filter1, tp_replace_in_columnFiltering, Label-free quantification, Visualisation, Prediction and recognition, FormattingMIT
metaquantome-function-worklowhttps://usegalaxy.eue5a89ef7b5f1c1d9https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumarproteomics, name:microgalaxy2024-11-212024-11-2133metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filterHeat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clusteringMIT
pAllori Amplicon 16S Pre-Processing and Taxonomy Classificationhttps://usegalaxy.eu466bdd8ba7b67264https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264Engy Nasr, Paul Zierepname:microgalaxy, name:16s, name:metagenomics, name:pallori2023-06-302024-11-217070ampvis2_load, trimmomatic, kraken2, tp_cut_tool, ampvis2_ordinate, unzip, taxonomy_krona_chart, collection_column_join, multiqc, lotus2, fastqc, __FLATTEN__, krakentools_kreport2krona, cutadapt, ampvis2_heatmapAggregation, Validation, Sequence composition calculation, Sequencing quality control, Visualisation, Analysis, Statistical calculation, Primer removal, Taxonomic classification, Read pre-processing, Sequence trimming, Sequence feature detection, DNA barcodingMIT
Cloud Aerosol MT-MG Contamination Filteringhttps://usegalaxy.euc09159d7aad0f264https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amatometagenomics, metatranscriptomics, name:microgalaxy2024-11-212024-11-2122seq_filter_by_id, kraken2, fastq_to_tabular, filter_tabular, bowtie2, recentrifugeTaxonomic classification, Read mapping, Expression analysis, Cross-assemblyMIT
Metatranscriptomics data analysishttps://usegalaxy.eufd90652d475ed739https://usegalaxy.eu/published/workflow?id=fd90652d475ed739Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffinname:microgalaxy, metatranscriptomics, microbiome2024-11-212024-11-2155bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqcSequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculationMIT
Cloud-Aerosole MT-MG Functional Profilinghttps://usegalaxy.eu63478edcea3f449ahttps://usegalaxy.eu/published/workflow?id=63478edcea3f449aEngy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amatometagenomics, metatranscriptomics, name:microgalaxy2024-11-212024-11-2144multiqc, bowtie2, featurecountsRead summarisation, Read mapping, Sequencing quality control, Validation, RNA-Seq quantificationMIT
Cloud-Aerosole MT-MG Pre-Processinghttps://usegalaxy.eu1ef76b7b86e15792https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amatometagenomics, metatranscriptomics, name:microgalaxy2024-11-212024-11-2166fastqc, multiqc, trimmomaticStatistical calculation, Sequence composition calculation, Sequencing quality control, ValidationMIT
Allele-based Pathogen Identification (release v0.1.2)https://usegalaxy.eu64abcddeb516a712https://usegalaxy.eu/published/workflow?id=64abcddeb516a712Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-10-312024-10-3111bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Taxonomy Profiling and Visualization with Kron (release v0.1)https://usegalaxy.euad8b6d73c9654305https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1)https://usegalaxy.euf6a763951d815944https://usegalaxy.eu/published/workflow?id=f6a763951d815944Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Nanopore Preprocessing (release v0.1)https://usegalaxy.eu344cd3a3c2ce5302https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302Bérénice Batut, Engy Nasr, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc2024-09-192024-09-1911Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mappedAggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, ValidationMIT
Gene-based Pathogen Identification (release v0.1)https://usegalaxy.eu77e5bbd317750915https://usegalaxy.eu/published/workflow?id=77e5bbd317750915Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2024-09-192024-09-1911fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
Allele-based Pathogen Identification (release v0.1)https://usegalaxy.eud215a2e554fd83bchttps://usegalaxy.eu/published/workflow?id=d215a2e554fd83bcEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Allele-based Pathogen Identification (release v0.1.1)https://usegalaxy.eucdf2f02428f5f83fhttps://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83fEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
pAllori WGShttps://usegalaxy.eu4f245ac304ab76d9https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9Engy Nasr, Paul Zierepname:pallori, name:microgalaxy, name:wgs2024-07-162024-07-281616bcftools_norm, __FLATTEN__, abricate, trimmomatic, regexColumn1, tp_awk_tool, ggplot2_heatmap, freebayes, Remove beginning1, multiqc, Grouping1, shovill, collection_column_join, fastqc, bowtie2, vcf2tsv, bcftools_view, snpSift_filterSequence composition calculation, Read mapping, Sequencing quality control, Variant calling, Visualisation, Antimicrobial resistance prediction, Statistical calculation, Genome assembly, ValidationMIT
MAGs workflowhttps://usegalaxy.eu97312d273b6e8bd9https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9name:microgalaxy2023-11-152024-07-111414concoct_extract_fasta_bins, maxbin2, Fasta_to_Contig2Bin, fastq_paired_end_interlacer, samtools_sort, __UNZIP_COLLECTION__, megahit, coverm_genome, concoct_merge_cut_up_clustering, drep_dereplicate, concoct, metabat2, semibin, quast, metabat2_jgi_summarize_bam_contig_depths, checkm_lineage_wf, das_tool, concoct_coverage_table, concoct_cut_up_fasta, bowtie2Sequence assembly, Genome comparison, Sequence composition calculation, Read mapping, Sequencing quality control, Genome assembly, Local alignment, Read binning, Sequence assembly validation, Genome annotation, Visualisation, Statistical calculation, Sequence clustering, Validation
PathoGFAIRhttps://usegalaxy.eu0dce37adb369492chttps://usegalaxy.eu/published/workflow?id=0dce37adb369492cEngy Nasr, Bérénice Batut, Paul Zierepname:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection2024-05-312024-07-039393MIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisationhttps://usegalaxy.eu376119528377a3aehttps://usegalaxy.eu/published/workflow?id=376119528377a3aeEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-04-032024-06-245858tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Allele-based Pathogen Identificationhttps://usegalaxy.eu09c7069ae409c362https://usegalaxy.eu/published/workflow?id=09c7069ae409c362Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2023-04-122024-06-247272bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Nanopore Preprocessinghttps://usegalaxy.eua705370bc2c13d5chttps://usegalaxy.eu/published/workflow?id=a705370bc2c13d5cBérénice Batut, Engy Nasr, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc2023-04-122024-06-24190190Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mappedAggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, ValidationMIT
Taxonomy Profiling and Visualization with Phinchhttps://usegalaxy.eub67b5ecd3305f830https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:gtn2023-04-122024-06-1988kraken_biom, kraken2, interactive_tool_phinchTaxonomic classificationMIT
metaQuantome_datacreation_workflowhttps://usegalaxy.eufc42cc9467c6ee8dhttps://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8dproteomics, name:microgalaxy2023-12-142024-06-1900msconvert, search_gui, peptide_shaker, Cut1, regex1, unipept, tp_replace_in_line, Remove beginning1, query_tabular, flashlfq, Filter1, tp_replace_in_columnFiltering, Label-free quantification, Visualisation, Prediction and recognition, Formatting
Gene-based Pathogen Identificationhttps://usegalaxy.eu585c21b7b1d864fchttps://usegalaxy.eu/published/workflow?id=585c21b7b1d864fcEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2023-04-132024-06-05142142fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
Taxonomy Profiling and Visualization with Kronahttps://usegalaxy.eu10101558b211a782https://usegalaxy.eu/published/workflow?id=10101558b211a782Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2023-05-112024-06-055858taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptoolhttps://usegalaxy.euc8bc4af6dd3b5d02https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02Engy Nasr, Bérénice Batutmicrobiome, nanopore, iwc, name:collection, name:microgalaxy2022-11-292024-04-04205205tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, interactive_tool_jupyter_notebook, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Mgnify MLhttps://usegalaxy.eu011f701c5a55bfdfhttps://usegalaxy.eu/published/workflow?id=011f701c5a55bfdfname:microgalaxy2023-10-102024-03-15128128interactive_tool_jupyter_notebook, __BUILD_LIST__
Normalizationhttps://usegalaxy.eu0603f0898211f806https://usegalaxy.eu/published/workflow?id=0603f0898211f806name:microgalaxy2023-09-252024-03-138080__EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__, map_param_value, __BUILD_LIST__, Grep1
WF1_Database_Generation_Workflowhttps://usegalaxy.eu7cfbf4b7bd3f30d3https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3name:clinicalmp, name:microgalaxy2023-12-142023-12-1411metanovo, fasta_merge_files_and_filter_unique_sequencesProtein identification, Expression analysis, Target-Decoy, de Novo sequencing, Tag-based peptide identification
WF2_Discovery-Workflowhttps://usegalaxy.eu8af41219411062adhttps://usegalaxy.eu/published/workflow?id=8af41219411062adname:microgalaxy, name:clinicalmp2023-12-142023-12-1411msconvert, fasta2tab, fasta_merge_files_and_filter_unique_sequences, search_gui, peptide_shaker, fasta_cli, Cut1, ident_params, Remove beginning1, query_tabular, Grouping1, dbbuilder, tp_cat, filter_tabular, Filter1, Grep1, maxquantFiltering, Clustering, Heat map generation, Protein quantification, Formatting, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting
WF3_VERIFICATION_WORKFLOWhttps://usegalaxy.eud87fc6685e47d27dhttps://usegalaxy.eu/published/workflow?id=d87fc6685e47d27dname:microgalaxy, name:clinicalmp2023-12-142023-12-1411pepquery2, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, Cut1, Remove beginning1, query_tabular, Grouping1, dbbuilder, Filter1, uniprotxml_downloader, tp_cat
WF4_Quantitation_Workflowhttps://usegalaxy.eua49275eb8b2b2ecbhttps://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecbname:clinicalmp, name:microgalaxy2023-12-142023-12-1411Cut1, Grep1, Grouping1, maxquantClustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting
WF5_Data_Interpretation_Worklowhttps://usegalaxy.eu755ede37d94dc456https://usegalaxy.eu/published/workflow?id=755ede37d94dc456name:microgalaxy, name:clinicalmp2023-12-142023-12-1411unipept, Grep1, msstatstmtVisualisation, Prediction and recognition
MetaG_extendedhttps://usegalaxy.eud57d41e306241396https://usegalaxy.eu/published/workflow?id=d57d41e306241396name:microgalaxy2023-12-142023-12-1411interproscan, fasplit, tp_awk_tool, maxbin2, trim_galore, quast, kofamscan, tp_grep_tool, fraggenescan, hmmer_hmmscan, sort1, fastqc, coverm_genome, checkm_lineage_wf, cat_bins, coverm_contig, tp_catConversion, Sequence generation, Probabilistic sequence generation, Sequence assembly, Coding region prediction, Sequencing quality control, Formatting, Visualisation, Data retrieval, Read pre-processing, Sequence trimming, Database search, Gene functional annotation, Protein feature detection, Sequence profile generation, Format validation, Sequence composition calculation, Sequence database search, Local alignment, Sequence assembly validation, Gene prediction, Sequence motif recognition, Primer removal, Statistical calculation, Taxonomic classification, Multiple sequence alignment, Sequence analysis, Validation
MetaPhttps://usegalaxy.eu01ac8bf9832789e2https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2name:microgalaxy2023-12-142023-12-1411maxquantClustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting
MetaThttps://usegalaxy.eu3733bcdf5b458be7https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7name:microgalaxy2023-12-142023-12-1411bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqcSequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculation
metaquantome-taxonomy-workflowhttps://usegalaxy.eu695f7defb516d80dhttps://usegalaxy.eu/published/workflow?id=695f7defb516d80dproteomics, name:microgalaxy2023-12-142023-12-1400metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filterHeat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clustering
metaquantome-function-worklowhttps://usegalaxy.eu4c364c6be27981bahttps://usegalaxy.eu/published/workflow?id=4c364c6be27981baproteomics, name:microgalaxy2023-12-142023-12-1400metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filterHeat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clustering
Metaproteomics_GTNhttps://usegalaxy.eu68967c922de149aehttps://usegalaxy.eu/published/workflow?id=68967c922de149aeproteomics, name:microgalaxy2023-12-142023-12-1400search_gui, peptide_shaker, unipept, query_tabular, sqlite_to_tabularVisualisation, Prediction and recognition
Ecoli Comparisonhttps://usegalaxy.eu0e492839192d26e0https://usegalaxy.eu/published/workflow?id=0e492839192d26e0assembly, name:microgalaxy2023-12-142023-12-1400lastz_wrapper_2, tp_grep_tool, fasta_filter_by_length, tp_sed_tool, datamash_ops, mergeCols1, tp_sort_header_tool, bedtools_complementbed, collapse_dataset, join1, addValue, random_lines1, fasta_compute_length, cat1, Cut1, bedtools_sortbed, Filter1, Grep1, bedtools_intersectbed, tp_catRead mapping, Mapping, Sequence alignment
Training: 16S rRNA Analysis with Nanopore Sequencing Readshttps://usegalaxy.eu08eb5e55109c4d9chttps://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9cmetagenomics, name:microgalaxy2023-12-142023-12-1400kraken2, porechop, tp_replace_in_line, taxonomy_krona_chart, fastp, multiqc, Remove beginning1, fastqc, datamash_reverseVisualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Sequence composition calculation, Sequencing quality control, Validation
Main Metatranscriptomics Analysishttps://usegalaxy.eu7a08ecdf23e0c7a3https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierepname:microgalaxy2023-12-142023-12-1400MIT
Copy Of GTN Training - Antibiotic Resistance Detectionhttps://usegalaxy.eu44e53ea319e07daahttps://usegalaxy.eu/published/workflow?id=44e53ea319e07daametagenomics, name:microgalaxy2023-12-142023-12-1400gfa_to_fa, bandage_image, nanoplot, racon, minimap2, PlasFlow, miniasm, staramr_search, unicyclerAggregation, Scatter plot plotting, Mapping assembly, De-novo assembly, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Genome assembly, Sequence analysis
Identification of the micro-organisms in a beer using Nanopore sequencinghttps://usegalaxy.eu0590554db9794d13https://usegalaxy.eu/published/workflow?id=0590554db9794d13Bérénice Batut, Teresa Müller, Polina Poluninametagenomics, name:microgalaxy2023-12-142023-12-1400kraken2, porechop, taxonomy_krona_chart, fastp, fastqc, Filter1, krakentools_kreport2kronaAggregation, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Sequence composition calculation, Sequencing quality controlMIT
workflow-generate-dataset-for-assembly-tutorialhttps://usegalaxy.euce5c16ac23c4fbb1https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1name:microgalaxy2023-12-142023-12-1400fastqc, seqtk_subseq, bamtools, filter_tabular, bg_uniq, ngsutils_bam_filter, megahit, random_lines1, bowtie2, cutadapt, tp_catData handling, Sequence alignment analysis, Sequence composition calculation, Read mapping, Sequencing quality control, Formatting, Variant calling, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Read pre-processing, Primer removal, Sequence file editing
Metagenomics assembly tutorial workflowhttps://usegalaxy.eu62c47e3c9d4f3aa3https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3name:microgalaxy2023-12-142023-12-1400megahit_contig2fastg, bandage_image, quast, collection_column_join, metaspades, megahit, bowtie2, bandage_infoSequence assembly validation, Visualisation, Genome assembly, Read mapping, Sequence assembly visualisation
WGS Part In "Analyses Of Metagenomics Data - The Global Picture"https://usegalaxy.euc2b7ec5aacfc6107https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107metagenomics, name:microgalaxy2023-12-142023-12-1400metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_tableVisualisation
Taxonomic Profiling and Visualization of Metagenomic Datahttps://usegalaxy.eu4f0daf8e9dd54127https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127Bérénice Batutmetagenomics, name:microgalaxy2023-12-142023-12-1400metaphlan, kraken2, interactive_tool_phinch, kraken_biom, est_abundance, taxonomy_krona_chart, __UNZIP_COLLECTION__, interactive_tool_pavian, krakentools_kreport2kronaAggregation, Visualisation, Statistical calculation, Taxonomic classification, Phylogenetic tree analysis, Nucleic acid sequence analysisMIT
Amplicon Tutorialhttps://usegalaxy.eu565c989730f68362https://usegalaxy.eu/published/workflow?id=565c989730f68362metagenomics, name:microgalaxy2023-12-142023-12-1400mothur_make_shared, mothur_cluster_split, krona-text, mothur_pre_cluster, mothur_screen_seqs, mothur_classify_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_otu, mothur_summary_seqs, mothur_merge_files, mothur_make_biom, mothur_align_seqsTaxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding
Microbial Variant Callinghttps://usegalaxy.eu515ef1601bc24a6chttps://usegalaxy.eu/published/workflow?id=515ef1601bc24a6cvariant-analysis, name:microgalaxy2023-12-142023-12-1400snippy, jbrowsePhylogenetic tree visualisation, Variant calling, Phylogenetic tree generation, Genome visualisation
Calling variants in non-diploid systemshttps://usegalaxy.eu291c36e1b18e9debhttps://usegalaxy.eu/published/workflow?id=291c36e1b18e9debvariant-analysis, name:microgalaxy2023-12-142023-12-1400bwa_mem, bamleftalign, picard_MarkDuplicates, picard_MergeSamFiles, vcffilter2, Cut1, freebayes, fastqc, bamFilter, vcf2tsvData handling, Sequence alignment analysis, Sequence composition calculation, Read mapping, Sequencing quality control, Formatting, Variant calling, Sequence alignment, Statistical calculation, Genome indexing, Generation
Training: 16S rRNA Sequencing With Mothur: Main Tutorialhttps://usegalaxy.euc67d2e75eeb4fd19https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19metagenomics, name:microgalaxy2023-12-142023-12-1400mothur_cluster_split, mothur_screen_seqs, mothur_count_seqs, mothur_dist_shared, mothur_classify_otu, taxonomy_krona_chart, mothur_count_groups, mothur_make_contigs, mothur_make_biom, mothur_make_shared, mothur_pre_cluster, mothur_summary_single, mothur_taxonomy_to_krona, mothur_remove_groups, mothur_venn, mothur_sub_sample, mothur_classify_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_summary_seqs, newick_display, mothur_rarefaction_single, mothur_get_groups, mothur_align_seqs, mothur_heatmap_sim, mothur_remove_lineage, mothur_tree_shared, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_dist_seqs, XY_Plot_1, mothur_seq_errorTaxonomic classification, Phylogenetic tree analysis, Sequencing quality control, Phylogenetic analysis, Phylogenetic tree generation, Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Sequence read processing, DNA barcoding
Comparative gene analysishttps://usegalaxy.eu86900be4282d4b1dhttps://usegalaxy.eu/published/workflow?id=86900be4282d4b1dAnton Nekrutenkovgp, genome-annotation, name:microgalaxy2023-12-142023-12-1400cat1, tp_split_on_column, Add_a_column1, regexColumn1, collapse_dataset, join1, Cut1, tab2fasta, rapidnj, rbc_mafft, bg_diamond, bg_diamond_view, Filter1, gops_intersect_1Multiple sequence alignment, Sequence alignment analysis, Phylogenetic tree generation
Unicycler traininghttps://usegalaxy.eu8f3ce55d44d9f369https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369assembly, name:microgalaxy2023-12-142023-12-1400quast, multiqc, prokka, fastqc, unicyclerAggregation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Visualisation, Gene prediction, Genome annotation, Statistical calculation, Genome assembly, Coding region prediction, Validation
Apollo Load Testhttps://usegalaxy.eu3c233cc56d4df8b0https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0genome-annotation, name:microgalaxy2023-12-142023-12-1400create_or_update, list_organism, iframe, jbrowse, create_accountGenome visualisation
Genome Annotation with Prokka [Feb 2020]https://usegalaxy.eue1894c36f1ab4ab4https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4genome-annotation, name:microgalaxy2023-12-142023-12-1400jbrowse, prokkaGenome visualisation, Gene prediction, Coding region prediction, Genome annotation
Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL)https://usegalaxy.eu152223c8aed27357https://usegalaxy.eu/published/workflow?id=152223c8aed27357wmdi, name:microgalaxy2023-12-142023-12-1400tp_easyjoin_tool, bg_column_arrange_by_header, bandage_image, minimap2, jbrowse, prokka, tbl2gff3, circos, staramr_search, circos_interval_to_tile, tp_cut_tool, regex1, tp_text_file_with_recurring_lines, ncbi_blastn_wrapper, tp_split_on_column, Add_a_column1, tp_sort_header_tool, gff2bed1, join1, tab2fasta, regex_replace, fasta_compute_length, deeptools_bam_coverage, circos_gc_skew, fasta2tab, trimmomatic, flye, Cut1, nanoplot, medaka_consensus_pipeline, PlasFlow, circos_wiggle_to_scatter, tp_head_tool, Filter1, Grep1, tp_catScatter plot plotting, Base-calling, De-novo assembly, Sequence assembly, Pairwise sequence alignment, Genome assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Variant calling, Genome visualisation, Gene prediction, Genome annotation, Sequence analysis, Sequence visualisation, Coding region prediction, Mapping assembly, Cross-assembly
Mtb phylogenyhttps://usegalaxy.eu875b3ca170ac12a1https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1evolution, name:microgalaxy2023-12-142023-12-1400interactive_tool_rstudio, raxmlPhylogenetic tree analysis, Sequence analysis
From VCFs to SNP distance matrixhttps://usegalaxy.eu6d333ed886aab471https://usegalaxy.eu/published/workflow?id=6d333ed886aab471evolution, name:microgalaxy2023-12-142023-12-1400bcftools_consensus, tb_variant_filter, snp_dists, snp_sites, tp_cat
From Fastqs to VCFs and BAMshttps://usegalaxy.eu3a8fde248a4d0383https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383evolution, name:microgalaxy2023-12-142023-12-1400__MERGE_COLLECTION__, tb_variant_filter, snippy, trimmomaticPhylogenetic tree visualisation, Variant calling, Phylogenetic tree generation
From BAMs to drug resistance prediction with TB-profilerhttps://usegalaxy.eud0d6dae0d1eecc21https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21evolution, name:microgalaxy2023-12-142023-12-1400tb_profiler_profile, samtools_view, tp_grep_tool, tp_sed_tool, __MERGE_COLLECTION__, tp_replace_in_line, addName, tp_catAntimicrobial resistance prediction
M. tuberculosis Variant Analysis tutorialhttps://usegalaxy.eu3ff4dbcc7a602e6bhttps://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6bPeter van Heusdenvariant-analysis, prokaryote, name:microgalaxy2023-12-142023-12-1400tb_profiler_profile, tbvcfreport, kraken2, trimmomatic, tb_variant_filter, snippy, multiqc, jbrowse, fastqcSequence composition calculation, Sequencing quality control, Variant calling, Phylogenetic tree generation, Genome visualisation, Antimicrobial resistance prediction, Statistical calculation, Taxonomic classification, Phylogenetic tree visualisation, ValidationMIT
Compute Allel Frequency Table from paired readshttps://usegalaxy.eu21a39ac4c1becb31https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31name:microgalaxy, hpylori2023-12-132023-12-1322bcftools_norm, tp_awk_tool, freebayes, bowtie2, vcf2tsv, bcftools_view, snpSift_filterRead mapping, Variant calling, Statistical calculation
Reference genome choice (indels, coverage, depth) for short readshttps://usegalaxy.eu61fe08fb3d5e83f8https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8name:microgalaxy, hpylori2023-10-272023-12-131313bcftools_norm, samtools_depth, collapse_dataset, collection_element_identifiers, vcf2tsv, freebayes, bowtie2, samtools_coverage, tp_catRead mapping, Variant calling, Statistical calculation
MGnify amplicon rRNA-prediction + ITShttps://usegalaxy.eu437704898229dfb6https://usegalaxy.eu/published/workflow?id=437704898229dfb6mgnify_amplicon_showcase, name:microgalaxy2023-12-122023-12-1311infernal_cmsearch, gops_concat_1, tp_awk_tool, bedtools_maskfastabed, mapseq, bedtools_getfastabed, biom_convert, taxonomy_krona_chart, query_tabular, cmsearch_deoverlapVisualisation, Comparison, Alignment, Nucleic acid feature detection, Mapping, Formatting, k-mer counting
MGnify amplicon QChttps://usegalaxy.eu8f415b0c409f56f7https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7mgnify_amplicon_showcase, name:microgalaxy2023-12-132023-12-1311prinseq, trimmomatic, tp_find_and_replace, fastq_dump, fastp, __UNZIP_COLLECTION__, cshl_fasta_formatter, multiqc, iuc_pear, fastqc, fastq_to_fasta_pythonData handling, Sequence merging, Sequence composition calculation, Sequencing quality control, Sequence contamination filtering, Read pre-processing, Sequence trimming, Statistical calculation, Validation
Cloud-Aerosole MT-MG Functional Profilinghttps://usegalaxy.eu4566262dd0acc8abhttps://usegalaxy.eu/published/workflow?id=4566262dd0acc8abmetagenomics, metatranscriptomics, name:microgalaxy2021-11-102023-12-0722multiqc, bowtie2, featurecountsRead summarisation, Read mapping, Sequencing quality control, Validation, RNA-Seq quantification
Cloud-Aerosole MT-MG Reference Gene Catalog Buildinghttps://usegalaxy.eu9b9e1e28f3683f92https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92metagenomics, metatranscriptomics, name:microgalaxy2021-11-012023-12-077272cat1, metagene_annotator, bg_diamond_makedb, metaeuk_easy_predict, translate_nucleotides, quast, kofamscan, bedtools_getfastabed, cd_hit, eggnog_mapper, multiqc, bg_diamond, dbbuilder, megahit, fastqc, bowtie2Sequence alignment analysis, Sequence annotation, Sequencing quality control, Fold recognition, Visualisation, Homology-based gene prediction, Query and retrieval, Genome assembly, Sequence clustering, Gene functional annotation, Sequence composition calculation, Read mapping, Sequence assembly validation, Genome annotation, Statistical calculation, Mapping, Sequence analysis, Information extraction, Validation
Cloud-Aerosole MT-MG Pre-Processinghttps://usegalaxy.eubb604ff5e010e7abhttps://usegalaxy.eu/published/workflow?id=bb604ff5e010e7abmetagenomics, metatranscriptomics, name:microgalaxy2021-11-012023-12-075151fastqc, multiqc, trimmomaticStatistical calculation, Sequence composition calculation, Sequencing quality control, Validation
Cloud Aerosol MT-MG Contamination Filteringhttps://usegalaxy.eubdc7cfaac0db2eabhttps://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eabmetagenomics, metatranscriptomics, name:microgalaxy2022-06-292023-12-072828seq_filter_by_id, kraken2, fastq_to_tabular, filter_tabular, bowtie2, recentrifugeTaxonomic classification, Read mapping, Expression analysis, Cross-assembly
Cloud-Aerosole MT-MG Taxonomic Profilinghttps://usegalaxy.eue69b555faa6bb962https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962metagenomics, metatranscriptomics, name:microgalaxy2022-09-032023-12-071818maaslin2, kraken2, interactive_tool_phinch, kraken_biom, recentrifugeFiltering, Visualisation, Expression analysis, Statistical calculation, Taxonomic classification, Cross-assembly, Standardisation and normalisation
pAllori ASiam Functional Information MThttps://usegalaxy.eua7a6d8ecc2795f58https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasrname:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:functionalprofiling2023-07-072023-07-0733combine_metaphlan2_humann2, Cut1, tp_find_and_replace, humann_renorm_table, humann, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table, Grep1, humann_rename_tableSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMIT
pAllori ASiam Community Profile MThttps://usegalaxy.eu05f5f040337786bfhttps://usegalaxy.eu/published/workflow?id=05f5f040337786bfEngy Nasr, Bérénice Batutname:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:communityprofiling2023-06-302023-07-0633metaphlan, graphlan_annotate, Cut1, graphlan, taxonomy_krona_chart, export2graphlanConversion, Phylogenetic tree analysis, Visualisation, Phylogenetic inference, Taxonomic classification, Phylogenetic tree visualisation, Nucleic acid sequence analysis, Phylogenetic tree editingMIT
pAllori ASiam Preprocessing MThttps://usegalaxy.eu72e3e5fdc766e24ahttps://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24aBérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasrname:microgalaxy, name:adaptedasiam, name:metatranscriptomics, name:preprocessing2023-06-302023-07-0622bg_sortmerna, fastq_paired_end_interlacer, multiqc, fastqc, __FLATTEN__, cutadaptSequence alignment analysis, Sequence similarity search, Sequence composition calculation, Sequencing quality control, Sequence comparison, Statistical calculation, Primer removal, Read pre-processing, Sequence trimming, ValidationMIT
MetaPhttps://usegalaxy.eu96d198ed953449fdhttps://usegalaxy.eu/published/workflow?id=96d198ed953449fdname:microgalaxy2020-01-302023-03-1622maxquantClustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting
MetaG_extendedhttps://usegalaxy.eu6158c3b5fc12044ehttps://usegalaxy.eu/published/workflow?id=6158c3b5fc12044ename:microgalaxy2023-02-102023-03-162222interproscan, fasplit, tp_awk_tool, maxbin2, trim_galore, quast, kofamscan, tp_grep_tool, fraggenescan, hmmer_hmmscan, sort1, fastqc, coverm_genome, checkm_lineage_wf, cat_bins, coverm_contig, tp_catConversion, Sequence generation, Probabilistic sequence generation, Sequence assembly, Coding region prediction, Sequencing quality control, Formatting, Visualisation, Data retrieval, Read pre-processing, Sequence trimming, Database search, Gene functional annotation, Protein feature detection, Sequence profile generation, Format validation, Sequence composition calculation, Sequence database search, Local alignment, Sequence assembly validation, Gene prediction, Sequence motif recognition, Primer removal, Statistical calculation, Taxonomic classification, Multiple sequence alignment, Sequence analysis, Validation
MetaThttps://usegalaxy.eu385cc7df70d7916bhttps://usegalaxy.eu/published/workflow?id=385cc7df70d7916bname:microgalaxy2020-01-272023-02-271616bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqcSequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculation
Allele-based Pathogen Identification (release v0.1.1)https://usegalaxy.org29ba77708cdafe0fhttps://usegalaxy.org/published/workflow?id=29ba77708cdafe0fEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-11-282024-11-2811bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Allele-based Pathogen Identification (release v0.1.2)https://usegalaxy.org6d778eeb176d563chttps://usegalaxy.org/published/workflow?id=6d778eeb176d563cEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-10-312024-10-3111bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Taxonomy Profiling and Visualization with Kron (release v0.1)https://usegalaxy.org4b5f6b5d4f36e38bhttps://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38bEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1)https://usegalaxy.org3ef08553982f6ffchttps://usegalaxy.org/published/workflow?id=3ef08553982f6ffcEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Gene-based Pathogen Identification (release v0.1)https://usegalaxy.org3f252e077e0bcce5https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2024-09-192024-09-1911fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisationhttps://usegalaxy.org2d3063882d8239ffhttps://usegalaxy.org/published/workflow?id=2d3063882d8239ffEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-07-032024-07-0311tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
PathoGFAIR (imported from uploaded file)https://usegalaxy.orge55593af91337a05https://usegalaxy.org/published/workflow?id=e55593af91337a05Engy Nasr, Bérénice Batut, Paul Zierepname:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection2024-07-032024-07-0300MIT
Taxonomy Profiling and Visualization with Kronahttps://usegalaxy.org8f5904693b5f74f4https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-06-252024-06-2511taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Gene-based Pathogen Identificationhttps://usegalaxy.orgcce88bc57b180d09https://usegalaxy.org/published/workflow?id=cce88bc57b180d09Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2024-06-252024-06-2511fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
Allele-based Pathogen Identificationhttps://usegalaxy.org38911ba6f66d80f6https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-06-252024-06-2511bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Nanopore Preprocessinghttps://usegalaxy.org574e42683dc3961bhttps://usegalaxy.org/published/workflow?id=574e42683dc3961bBérénice Batut, Engy Nasr, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc2024-06-252024-06-2511Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mappedAggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, ValidationMIT
Allele-based Pathogen Identification (release v0.1.2)https://usegalaxy.org.au857e482acfcb2dbahttps://usegalaxy.org.au/published/workflow?id=857e482acfcb2dbaEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-10-312024-10-3111bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Taxonomy Profiling and Visualization with Kron (release v0.1)https://usegalaxy.org.au131636a795bac485https://usegalaxy.org.au/published/workflow?id=131636a795bac485Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1)https://usegalaxy.org.aub60922a253df6654https://usegalaxy.org.au/published/workflow?id=b60922a253df6654Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-09-192024-09-1911tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Nanopore Preprocessing (release v0.1)https://usegalaxy.org.au69d91340fc7effa2https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2Bérénice Batut, Engy Nasr, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc2024-09-192024-09-1911Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mappedAggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, ValidationMIT
Gene-based Pathogen Identification (release v0.1)https://usegalaxy.org.au084bb76cf47d7060https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2024-09-192024-09-1911fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
PathoGFAIR (imported from uploaded file)https://usegalaxy.org.auf5f9808fb50b6f2chttps://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2cEngy Nasr, Bérénice Batut, Paul Zierepname:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection2024-07-032024-07-0300MIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisationhttps://usegalaxy.org.aueda40b58616a0fe4https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-07-032024-07-0311tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_joinPhylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generationMIT
Allele-based Pathogen Identificationhttps://usegalaxy.org.au244ea5e94237ebadhttps://usegalaxy.org.au/published/workflow?id=244ea5e94237ebadEngy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-06-252024-06-2511bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filterPairwise sequence alignment, Variant callingMIT
Gene-based Pathogen Identificationhttps://usegalaxy.org.auef8c22c2525063a2https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:pathogfair, name:iwc, name:microgalaxy2024-06-252024-06-2511fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assemblyMIT
Taxonomy Profiling and Visualization with Kronahttps://usegalaxy.org.aud9ba165e6ae55417https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:iwc2024-06-252024-06-2511taxonomy_krona_chart, krakentools_kreport2krona, kraken2Aggregation, Visualisation, Taxonomic classificationMIT
Nanopore Preprocessinghttps://usegalaxy.org.au25d52afddaa3451bhttps://usegalaxy.org.au/published/workflow?id=25d52afddaa3451bBérénice Batut, Engy Nasr, Paul Zierepname:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc2024-06-252024-06-2511Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mappedAggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, ValidationMIT
- -
\ No newline at end of file diff --git a/communities/microgalaxy/resources/workflows.tsv b/communities/microgalaxy/resources/workflows.tsv deleted file mode 100644 index c0784ebb..00000000 --- a/communities/microgalaxy/resources/workflows.tsv +++ /dev/null @@ -1,136 +0,0 @@ -Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects -Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "Prepare alpha diversity summary file (paste sample identifiers and Simpson results) -Paste1, kraken2, krakentools_beta_diversity, collection_element_identifiers, regex1, add_line_to_file, Prepare alpha diversity summary file (paste Simpson and Fisher results) -Paste1, Prepare alpha diversity summary file -Paste1, est_abundance, cat_multiple, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" -Show tail1, taxonomy_krona_chart, collection_column_join, krakentools_alpha_diversity, __RELABEL_FROM_FILE__, Extract column name and fraction_total_reads from Bracken report -Cut1, krakentools_kreport2krona, krakentools_combine_kreports" Aggregation, Visualisation, Statistical calculation, Taxonomic classification Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics -AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2024-11-14 2 2 36.0 , staramr_search, hamronize_tool, abricate, tp_find_and_replace, __MERGE_COLLECTION__, datamash_ops, tp_text_file_with_recurring_lines, hamronize_summarize, tp_split_on_column, collapse_dataset, cat_multi_datasets, addValue, __APPLY_RULES__, cat1, Cut1, cast, shovill, Grep1 Data handling, Antimicrobial resistance prediction, Genome assembly, Parsing MIT Seq4AMR, ErasmusMC Clinical Bioinformatics -bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=7 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2024-11-26 2024-11-26 7 7 7.0 refseq_masher_matches, tooldistillator_summarize, bandage_image, quast, shovill, tooldistillator, bandage_info Data handling, Sequence assembly validation, Parsing, Visualisation, Genome assembly, Sequence assembly visualisation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) -quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=8 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-11-23 2024-11-23 8 8 6.0 tooldistillator_summarize, kraken2, est_abundance, fastp, tooldistillator, recentrifuge Data handling, Expression analysis, Sequencing quality control, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Cross-assembly, Parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) -Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2024-09-09 1 1 10.0 hamronize_tool, abricate, collapse_dataset, tp_find_and_replace, shovill, hamronize_summarize, staramr_search Data handling, Antimicrobial resistance prediction, Genome assembly, Parsing GPL-3.0 Seq4AMR -bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2024-10-26 2024-10-26 9 9 6.0 tooldistillator_summarize, bakta, integron_finder, plasmidfinder, isescan, tooldistillator Protein feature detection, Data handling, Nucleic acid feature detection, Multilocus sequence typing, Genome annotation, Sequence motif recognition, Scaffolding, Structural variation detection, Genome assembly, Parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) -amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=7 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2024-10-26 2024-10-27 7 7 5.0 abricate, tooldistillator_summarize, staramr_search, amrfinderplus, tooldistillator Data handling, Antimicrobial resistance prediction, Parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) -Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2024-04-05 1 1 17.0 , metaphlan2krona, metaphlan2, Cut1, taxonomy_krona_chart, humann2_renorm_table, humann2, humann2_regroup_table, merge_metaphlan_tables Phylogenetic tree analysis, Nucleic acid sequence analysis, Visualisation Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics -Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 4.0 mothur_tree_shared, mothur_dist_shared, mothur_heatmap_sim, newick_display Taxonomic classification, Phylogenetic tree analysis, Sequencing quality control, Phylogenetic analysis, Phylogenetic tree generation, Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 3.0 mothur_rarefaction_single, XY_Plot_1, mothur_summary_single Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_make_shared, mothur_cluster_split, mothur_sub_sample, mothur_classify_otu, mothur_count_groups Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 2.0 mothur_remove_lineage, mothur_classify_seqs Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 5.0 mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_screen_seqs Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2023-11-09 1 1 9.0 mothur_pre_cluster, mothur_screen_seqs, mothur_remove_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_summary_seqs Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding CC-BY-4.0 QCIF Bioinformatics -pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=2 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2024-06-22 2024-06-22 2 2 40.0 " - Cut1, samtools_view, fastp, - __SORTLIST__, samtools_merge, ivar_consensus, split_file_to_collection, - __ZIP_COLLECTION__, - __APPLY_RULES__, - Grep1, tp_sed_tool, EMBOSS: maskseq51, datamash_ops, samtools_stats, - param_value_from_file, - __FILTER_FAILED_DATASETS__, compose_text_param, qualimap_bamqc, fasta_compute_length, ivar_trim, bwa_mem, - __FLATTEN__, collection_element_identifiers, multiqc, tp_cat" Sequence alignment analysis, Read mapping, Sequencing quality control, Local alignment, Sequence alignment, Genome indexing, Sequence contamination filtering, Global alignment, Sequence analysis, Generation, Validation MIT Intergalactic Workflow Commission (IWC) -3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2023-02-13 1 1 2.0 fastp, shovill Sequencing quality control, Sequence contamination filtering, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory -2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2023-02-13 1 1 7.0 fasta_merge_files_and_filter_unique_sequences, minimap2, samtools_stats, ngsutils_bam_filter, shovill, picard_SamToFastq, ncbi_blastn_wrapper Variant calling, Sequence contamination filtering, Read pre-processing, Genome assembly, Sequencing quality control, Pairwise sequence alignment, Formatting Apache-2.0 Integrated and Urban Plant Pathology Laboratory -GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2023-02-13 1 1 12.0 gfa_to_fa, bandage_image, nanoplot, staramr_search, minimap2, PlasFlow, miniasm, racon, unicycler Aggregation, Scatter plot plotting, De-novo assembly, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Sequence analysis, Genome assembly, Mapping assembly Microbiology CC-BY-4.0 Galaxy Training Network -1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2023-02-13 1 1 3.0 taxonomy_krona_chart, Kraken2Tax, kraken2 Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory -1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2023-02-13 1 1 3.0 taxonomy_krona_chart, Kraken2Tax, kraken2 Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory -Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 cat1, tp_split_on_column, Add_a_column1, regexColumn1, collapse_dataset, join1, Cut1, tab2fasta, rapidnj, rbc_mafft, bg_diamond, bg_diamond_view, Filter1, gops_intersect_1 Multiple sequence alignment, Sequence alignment analysis, Phylogenetic tree generation -pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 fastqc, __FILTER_FAILED_DATASETS__, rna_star, featurecounts, multiqc, collection_column_join, umi_tools_extract Read summarisation, Statistical calculation, Sequence composition calculation, Sequencing quality control, Sequence alignment, Validation, RNA-Seq quantification MIT -Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, unipept, query_tabular, sqlite_to_tabular Visualisation, Prediction and recognition MIT -Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__, map_param_value, __BUILD_LIST__, Grep1 MIT -metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 msconvert, search_gui, peptide_shaker, Cut1, regex1, unipept, tp_replace_in_line, Remove beginning1, query_tabular, flashlfq, Filter1, tp_replace_in_column Filtering, Label-free quantification, Visualisation, Prediction and recognition, Formatting MIT -metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filter Heat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clustering MIT -pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 ampvis2_load, trimmomatic, kraken2, tp_cut_tool, ampvis2_ordinate, unzip, taxonomy_krona_chart, collection_column_join, multiqc, lotus2, fastqc, __FLATTEN__, krakentools_kreport2krona, cutadapt, ampvis2_heatmap Aggregation, Validation, Sequence composition calculation, Sequencing quality control, Visualisation, Analysis, Statistical calculation, Primer removal, Taxonomic classification, Read pre-processing, Sequence trimming, Sequence feature detection, DNA barcoding MIT -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 seq_filter_by_id, kraken2, fastq_to_tabular, filter_tabular, bowtie2, recentrifuge Taxonomic classification, Read mapping, Expression analysis, Cross-assembly MIT -Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqc Sequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculation MIT - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, bowtie2, featurecounts Read summarisation, Read mapping, Sequencing quality control, Validation, RNA-Seq quantification MIT -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 fastqc, multiqc, trimmomatic Statistical calculation, Sequence composition calculation, Sequencing quality control, Validation MIT -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.eu 64abcddeb516a712 https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2024-09-19 1 1 Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mapped Aggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Validation MIT -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.eu 77e5bbd317750915 https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -Allele-based Pathogen Identification (release v0.1) https://usegalaxy.eu d215a2e554fd83bc https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.eu cdf2f02428f5f83f https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microgalaxy, name:wgs 2024-07-16 2024-07-28 16 16 bcftools_norm, __FLATTEN__, abricate, trimmomatic, regexColumn1, tp_awk_tool, ggplot2_heatmap, freebayes, Remove beginning1, multiqc, Grouping1, shovill, collection_column_join, fastqc, bowtie2, vcf2tsv, bcftools_view, snpSift_filter Sequence composition calculation, Read mapping, Sequencing quality control, Variant calling, Visualisation, Antimicrobial resistance prediction, Statistical calculation, Genome assembly, Validation MIT -MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microgalaxy 2023-11-15 2024-07-11 14 14 concoct_extract_fasta_bins, maxbin2, Fasta_to_Contig2Bin, fastq_paired_end_interlacer, samtools_sort, __UNZIP_COLLECTION__, megahit, coverm_genome, concoct_merge_cut_up_clustering, drep_dereplicate, concoct, metabat2, semibin, quast, metabat2_jgi_summarize_bam_contig_depths, checkm_lineage_wf, das_tool, concoct_coverage_table, concoct_cut_up_fasta, bowtie2 Sequence assembly, Genome comparison, Sequence composition calculation, Read mapping, Sequencing quality control, Genome assembly, Local alignment, Read binning, Sequence assembly validation, Genome annotation, Visualisation, Statistical calculation, Sequence clustering, Validation -PathoGFAIR https://usegalaxy.eu 0dce37adb369492c https://usegalaxy.eu/published/workflow?id=0dce37adb369492c Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-05-31 2024-07-03 93 93 MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-04-03 2024-06-24 58 58 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-04-12 2024-06-24 72 72 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2023-04-12 2024-06-24 190 190 Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mapped Aggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Validation MIT -Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:gtn 2023-04-12 2024-06-19 8 8 kraken_biom, kraken2, interactive_tool_phinch Taxonomic classification MIT -metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microgalaxy 2023-12-14 2024-06-19 0 0 msconvert, search_gui, peptide_shaker, Cut1, regex1, unipept, tp_replace_in_line, Remove beginning1, query_tabular, flashlfq, Filter1, tp_replace_in_column Filtering, Label-free quantification, Visualisation, Prediction and recognition, Formatting -Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2023-04-13 2024-06-05 142 142 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-05-11 2024-06-05 58 58 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, iwc, name:collection, name:microgalaxy 2022-11-29 2024-04-04 205 205 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, interactive_tool_jupyter_notebook, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microgalaxy 2023-10-10 2024-03-15 128 128 interactive_tool_jupyter_notebook, __BUILD_LIST__ -Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microgalaxy 2023-09-25 2024-03-13 80 80 __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__, map_param_value, __BUILD_LIST__, Grep1 -WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences Protein identification, Expression analysis, Target-Decoy, de Novo sequencing, Tag-based peptide identification -WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 msconvert, fasta2tab, fasta_merge_files_and_filter_unique_sequences, search_gui, peptide_shaker, fasta_cli, Cut1, ident_params, Remove beginning1, query_tabular, Grouping1, dbbuilder, tp_cat, filter_tabular, Filter1, Grep1, maxquant Filtering, Clustering, Heat map generation, Protein quantification, Formatting, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting -WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 pepquery2, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, Cut1, Remove beginning1, query_tabular, Grouping1, dbbuilder, Filter1, uniprotxml_downloader, tp_cat -WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 Cut1, Grep1, Grouping1, maxquant Clustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting -WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 unipept, Grep1, msstatstmt Visualisation, Prediction and recognition -MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 interproscan, fasplit, tp_awk_tool, maxbin2, trim_galore, quast, kofamscan, tp_grep_tool, fraggenescan, hmmer_hmmscan, sort1, fastqc, coverm_genome, checkm_lineage_wf, cat_bins, coverm_contig, tp_cat Conversion, Sequence generation, Probabilistic sequence generation, Sequence assembly, Coding region prediction, Sequencing quality control, Formatting, Visualisation, Data retrieval, Read pre-processing, Sequence trimming, Database search, Gene functional annotation, Protein feature detection, Sequence profile generation, Format validation, Sequence composition calculation, Sequence database search, Local alignment, Sequence assembly validation, Gene prediction, Sequence motif recognition, Primer removal, Statistical calculation, Taxonomic classification, Multiple sequence alignment, Sequence analysis, Validation -MetaP https://usegalaxy.eu 01ac8bf9832789e2 https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 name:microgalaxy 2023-12-14 2023-12-14 1 1 maxquant Clustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting -MetaT https://usegalaxy.eu 3733bcdf5b458be7 https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 name:microgalaxy 2023-12-14 2023-12-14 1 1 bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqc Sequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculation -metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filter Heat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clustering -metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_sample, metaquantome_db, metaquantome_filter Heat map generation, Statistical inference, Principal component visualisation, Visualisation, Query and retrieval, Differential protein expression analysis, Filtering, Quantification, Indexing, Functional clustering -Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 search_gui, peptide_shaker, unipept, query_tabular, sqlite_to_tabular Visualisation, Prediction and recognition -Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 lastz_wrapper_2, tp_grep_tool, fasta_filter_by_length, tp_sed_tool, datamash_ops, mergeCols1, tp_sort_header_tool, bedtools_complementbed, collapse_dataset, join1, addValue, random_lines1, fasta_compute_length, cat1, Cut1, bedtools_sortbed, Filter1, Grep1, bedtools_intersectbed, tp_cat Read mapping, Mapping, Sequence alignment -Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken2, porechop, tp_replace_in_line, taxonomy_krona_chart, fastp, multiqc, Remove beginning1, fastqc, datamash_reverse Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Sequence composition calculation, Sequencing quality control, Validation -Main Metatranscriptomics Analysis https://usegalaxy.eu 7a08ecdf23e0c7a3 https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep name:microgalaxy 2023-12-14 2023-12-14 0 0 MIT -Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 gfa_to_fa, bandage_image, nanoplot, racon, minimap2, PlasFlow, miniasm, staramr_search, unicycler Aggregation, Scatter plot plotting, Mapping assembly, De-novo assembly, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Genome assembly, Sequence analysis -Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken2, porechop, taxonomy_krona_chart, fastp, fastqc, Filter1, krakentools_kreport2krona Aggregation, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Sequence composition calculation, Sequencing quality control MIT -workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microgalaxy 2023-12-14 2023-12-14 0 0 fastqc, seqtk_subseq, bamtools, filter_tabular, bg_uniq, ngsutils_bam_filter, megahit, random_lines1, bowtie2, cutadapt, tp_cat Data handling, Sequence alignment analysis, Sequence composition calculation, Read mapping, Sequencing quality control, Formatting, Variant calling, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Read pre-processing, Primer removal, Sequence file editing -Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microgalaxy 2023-12-14 2023-12-14 0 0 megahit_contig2fastg, bandage_image, quast, collection_column_join, metaspades, megahit, bowtie2, bandage_info Sequence assembly validation, Visualisation, Genome assembly, Read mapping, Sequence assembly visualisation -"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_table Visualisation -Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaphlan, kraken2, interactive_tool_phinch, kraken_biom, est_abundance, taxonomy_krona_chart, __UNZIP_COLLECTION__, interactive_tool_pavian, krakentools_kreport2krona Aggregation, Visualisation, Statistical calculation, Taxonomic classification, Phylogenetic tree analysis, Nucleic acid sequence analysis MIT -Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_make_shared, mothur_cluster_split, krona-text, mothur_pre_cluster, mothur_screen_seqs, mothur_classify_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_otu, mothur_summary_seqs, mothur_merge_files, mothur_make_biom, mothur_align_seqs Taxonomic classification, Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence clustering, Sequence read processing, DNA barcoding -Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, jbrowse Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation, Genome visualisation -Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 bwa_mem, bamleftalign, picard_MarkDuplicates, picard_MergeSamFiles, vcffilter2, Cut1, freebayes, fastqc, bamFilter, vcf2tsv Data handling, Sequence alignment analysis, Sequence composition calculation, Read mapping, Sequencing quality control, Formatting, Variant calling, Sequence alignment, Statistical calculation, Genome indexing, Generation -Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_cluster_split, mothur_screen_seqs, mothur_count_seqs, mothur_dist_shared, mothur_classify_otu, taxonomy_krona_chart, mothur_count_groups, mothur_make_contigs, mothur_make_biom, mothur_make_shared, mothur_pre_cluster, mothur_summary_single, mothur_taxonomy_to_krona, mothur_remove_groups, mothur_venn, mothur_sub_sample, mothur_classify_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_summary_seqs, newick_display, mothur_rarefaction_single, mothur_get_groups, mothur_align_seqs, mothur_heatmap_sim, mothur_remove_lineage, mothur_tree_shared, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_dist_seqs, XY_Plot_1, mothur_seq_error Taxonomic classification, Phylogenetic tree analysis, Sequencing quality control, Phylogenetic analysis, Phylogenetic tree generation, Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Sequence read processing, DNA barcoding -Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 cat1, tp_split_on_column, Add_a_column1, regexColumn1, collapse_dataset, join1, Cut1, tab2fasta, rapidnj, rbc_mafft, bg_diamond, bg_diamond_view, Filter1, gops_intersect_1 Multiple sequence alignment, Sequence alignment analysis, Phylogenetic tree generation -Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 quast, multiqc, prokka, fastqc, unicycler Aggregation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Visualisation, Gene prediction, Genome annotation, Statistical calculation, Genome assembly, Coding region prediction, Validation -Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 create_or_update, list_organism, iframe, jbrowse, create_account Genome visualisation -Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, prokka Genome visualisation, Gene prediction, Coding region prediction, Genome annotation -Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 tp_easyjoin_tool, bg_column_arrange_by_header, bandage_image, minimap2, jbrowse, prokka, tbl2gff3, circos, staramr_search, circos_interval_to_tile, tp_cut_tool, regex1, tp_text_file_with_recurring_lines, ncbi_blastn_wrapper, tp_split_on_column, Add_a_column1, tp_sort_header_tool, gff2bed1, join1, tab2fasta, regex_replace, fasta_compute_length, deeptools_bam_coverage, circos_gc_skew, fasta2tab, trimmomatic, flye, Cut1, nanoplot, medaka_consensus_pipeline, PlasFlow, circos_wiggle_to_scatter, tp_head_tool, Filter1, Grep1, tp_cat Scatter plot plotting, Base-calling, De-novo assembly, Sequence assembly, Pairwise sequence alignment, Genome assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Variant calling, Genome visualisation, Gene prediction, Genome annotation, Sequence analysis, Sequence visualisation, Coding region prediction, Mapping assembly, Cross-assembly -Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 interactive_tool_rstudio, raxml Phylogenetic tree analysis, Sequence analysis -From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 bcftools_consensus, tb_variant_filter, snp_dists, snp_sites, tp_cat -From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 __MERGE_COLLECTION__, tb_variant_filter, snippy, trimmomatic Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation -From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, samtools_view, tp_grep_tool, tp_sed_tool, __MERGE_COLLECTION__, tp_replace_in_line, addName, tp_cat Antimicrobial resistance prediction -M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microgalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, tbvcfreport, kraken2, trimmomatic, tb_variant_filter, snippy, multiqc, jbrowse, fastqc Sequence composition calculation, Sequencing quality control, Variant calling, Phylogenetic tree generation, Genome visualisation, Antimicrobial resistance prediction, Statistical calculation, Taxonomic classification, Phylogenetic tree visualisation, Validation MIT -Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bcftools_norm, tp_awk_tool, freebayes, bowtie2, vcf2tsv, bcftools_view, snpSift_filter Read mapping, Variant calling, Statistical calculation -Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bcftools_norm, samtools_depth, collapse_dataset, collection_element_identifiers, vcf2tsv, freebayes, bowtie2, samtools_coverage, tp_cat Read mapping, Variant calling, Statistical calculation -MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 mgnify_amplicon_showcase, name:microgalaxy 2023-12-12 2023-12-13 1 1 infernal_cmsearch, gops_concat_1, tp_awk_tool, bedtools_maskfastabed, mapseq, bedtools_getfastabed, biom_convert, taxonomy_krona_chart, query_tabular, cmsearch_deoverlap Visualisation, Comparison, Alignment, Nucleic acid feature detection, Mapping, Formatting, k-mer counting -MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 mgnify_amplicon_showcase, name:microgalaxy 2023-12-13 2023-12-13 1 1 prinseq, trimmomatic, tp_find_and_replace, fastq_dump, fastp, __UNZIP_COLLECTION__, cshl_fasta_formatter, multiqc, iuc_pear, fastqc, fastq_to_fasta_python Data handling, Sequence merging, Sequence composition calculation, Sequencing quality control, Sequence contamination filtering, Read pre-processing, Sequence trimming, Statistical calculation, Validation - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-10 2023-12-07 2 2 multiqc, bowtie2, featurecounts Read summarisation, Read mapping, Sequencing quality control, Validation, RNA-Seq quantification -Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 72 72 cat1, metagene_annotator, bg_diamond_makedb, metaeuk_easy_predict, translate_nucleotides, quast, kofamscan, bedtools_getfastabed, cd_hit, eggnog_mapper, multiqc, bg_diamond, dbbuilder, megahit, fastqc, bowtie2 Sequence alignment analysis, Sequence annotation, Sequencing quality control, Fold recognition, Visualisation, Homology-based gene prediction, Query and retrieval, Genome assembly, Sequence clustering, Gene functional annotation, Sequence composition calculation, Read mapping, Sequence assembly validation, Genome annotation, Statistical calculation, Mapping, Sequence analysis, Information extraction, Validation -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 51 51 fastqc, multiqc, trimmomatic Statistical calculation, Sequence composition calculation, Sequencing quality control, Validation -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microgalaxy 2022-06-29 2023-12-07 28 28 seq_filter_by_id, kraken2, fastq_to_tabular, filter_tabular, bowtie2, recentrifuge Taxonomic classification, Read mapping, Expression analysis, Cross-assembly -Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microgalaxy 2022-09-03 2023-12-07 18 18 maaslin2, kraken2, interactive_tool_phinch, kraken_biom, recentrifuge Filtering, Visualisation, Expression analysis, Statistical calculation, Taxonomic classification, Cross-assembly, Standardisation and normalisation -pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:functionalprofiling 2023-07-07 2023-07-07 3 3 combine_metaphlan2_humann2, Cut1, tp_find_and_replace, humann_renorm_table, humann, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table, Grep1, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT - pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:communityprofiling 2023-06-30 2023-07-06 3 3 metaphlan, graphlan_annotate, Cut1, graphlan, taxonomy_krona_chart, export2graphlan Conversion, Phylogenetic tree analysis, Visualisation, Phylogenetic inference, Taxonomic classification, Phylogenetic tree visualisation, Nucleic acid sequence analysis, Phylogenetic tree editing MIT - pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:adaptedasiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2023-07-06 2 2 bg_sortmerna, fastq_paired_end_interlacer, multiqc, fastqc, __FLATTEN__, cutadapt Sequence alignment analysis, Sequence similarity search, Sequence composition calculation, Sequencing quality control, Sequence comparison, Statistical calculation, Primer removal, Read pre-processing, Sequence trimming, Validation MIT -MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Clustering, Heat map generation, Protein quantification, Imputation, Standardisation and normalisation, Visualisation, Statistical calculation, Principal component plotting -MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 interproscan, fasplit, tp_awk_tool, maxbin2, trim_galore, quast, kofamscan, tp_grep_tool, fraggenescan, hmmer_hmmscan, sort1, fastqc, coverm_genome, checkm_lineage_wf, cat_bins, coverm_contig, tp_cat Conversion, Sequence generation, Probabilistic sequence generation, Sequence assembly, Coding region prediction, Sequencing quality control, Formatting, Visualisation, Data retrieval, Read pre-processing, Sequence trimming, Database search, Gene functional annotation, Protein feature detection, Sequence profile generation, Format validation, Sequence composition calculation, Sequence database search, Local alignment, Sequence assembly validation, Gene prediction, Sequence motif recognition, Primer removal, Statistical calculation, Taxonomic classification, Multiple sequence alignment, Sequence analysis, Validation -MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 bg_sortmerna, trim_galore, __UNZIP_COLLECTION__, kallisto_quant, collection_column_join, fastqc Sequence alignment analysis, Sequence similarity search, Sequence composition calculation, Gene expression profiling, Sequencing quality control, Sequence comparison, Primer removal, Read pre-processing, Sequence trimming, Statistical calculation -Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.org 29ba77708cdafe0f https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-11-28 2024-11-28 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org 6d778eeb176d563c https://usegalaxy.org/published/workflow?id=6d778eeb176d563c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org 4b5f6b5d4f36e38b https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org 3ef08553982f6ffc https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org 3f252e077e0bcce5 https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org 2d3063882d8239ff https://usegalaxy.org/published/workflow?id=2d3063882d8239ff Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -PathoGFAIR (imported from uploaded file) https://usegalaxy.org e55593af91337a05 https://usegalaxy.org/published/workflow?id=e55593af91337a05 Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-07-03 2024-07-03 0 0 MIT -Taxonomy Profiling and Visualization with Krona https://usegalaxy.org 8f5904693b5f74f4 https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Gene-based Pathogen Identification https://usegalaxy.org cce88bc57b180d09 https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -Allele-based Pathogen Identification https://usegalaxy.org 38911ba6f66d80f6 https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Nanopore Preprocessing https://usegalaxy.org 574e42683dc3961b https://usegalaxy.org/published/workflow?id=574e42683dc3961b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mapped Aggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Validation MIT -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org.au 857e482acfcb2dba https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2024-10-31 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org.au 131636a795bac485 https://usegalaxy.org.au/published/workflow?id=131636a795bac485 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org.au b60922a253df6654 https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2024-09-19 1 1 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Nanopore Preprocessing (release v0.1) https://usegalaxy.org.au 69d91340fc7effa2 https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2024-09-19 1 1 Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mapped Aggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Validation MIT -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org.au 084bb76cf47d7060 https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2024-09-19 1 1 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -PathoGFAIR (imported from uploaded file) https://usegalaxy.org.au f5f9808fb50b6f2c https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-07-03 2024-07-03 0 0 MIT -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org.au eda40b58616a0fe4 https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 tp_multijoin_tool, bedtools_getfastabed, ggplot2_heatmap, regex1, Grouping1, clustalw, tp_split_on_column, fasttree, __FILTER_FAILED_DATASETS__, collapse_dataset, tab2fasta, newick_display, tp_replace_in_column, fasta2tab, fasta_merge_files_and_filter_unique_sequences, regexColumn1, Count1, Cut1, __FILTER_EMPTY_DATASETS__, tp_sorted_uniq, Remove beginning1, collection_column_join Phylogenetic tree generation (maximum likelihood and Bayesian methods), Visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Mapping, Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation MIT -Allele-based Pathogen Identification https://usegalaxy.org.au 244ea5e94237ebad https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 bcftools_norm, samtools_depth, table_compute, collapse_dataset, tp_cut_tool, Cut1, clair3, snpSift_extractFields, bcftools_consensus, Count1, regexColumn1, minimap2, Paste1, Remove beginning1, tp_head_tool, samtools_coverage, CONVERTER_gz_to_uncompressed, snpSift_filter Pairwise sequence alignment, Variant calling MIT -Gene-based Pathogen Identification https://usegalaxy.org.au ef8c22c2525063a2 https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 fasta2tab, abricate, flye, collection_element_identifiers, tp_find_and_replace, bandage_image, param_value_from_file, tab2fasta, medaka_consensus_pipeline, compose_text_param, split_file_to_collection, __BUILD_LIST__ Base-calling, De-novo assembly, Sequence assembly, Variant calling, Sequence assembly visualisation, Antimicrobial resistance prediction, Genome assembly, Mapping assembly, Cross-assembly MIT -Taxonomy Profiling and Visualization with Krona https://usegalaxy.org.au d9ba165e6ae55417 https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 taxonomy_krona_chart, krakentools_kreport2krona, kraken2 Aggregation, Visualisation, Taxonomic classification MIT -Nanopore Preprocessing https://usegalaxy.org.au 25d52afddaa3451b https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 Add_a_column1, porechop, collapse_dataset, __FILTER_FAILED_DATASETS__, samtools_fastx, kraken2, Cut1, nanoplot, krakentools_extract_kraken_reads, regexColumn1, minimap2, fastp, multiqc, collection_column_join, fastqc, Grep1, bamtools_split_mapped Aggregation, Data handling, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Validation MIT From bdff789b0c014eb7404cbe754fa79b8a79ac7f30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sun, 22 Dec 2024 18:23:38 +0100 Subject: [PATCH 5/5] Update workflow tests --- .../metadata/test_workflow_status.tsv | 12 + .../resources/test_curated_workflows.tsv | 12 + .../microgalaxy/resources/test_workflows.json | 434 ++++++++++++++++++ .../microgalaxy/resources/test_workflows.tsv | 24 +- sources/bin/extract_galaxy_workflows.py | 5 +- sources/bin/get_community_workflows.sh | 16 +- 6 files changed, 483 insertions(+), 20 deletions(-) create mode 100644 communities/microgalaxy/metadata/test_workflow_status.tsv create mode 100644 communities/microgalaxy/resources/test_curated_workflows.tsv create mode 100644 communities/microgalaxy/resources/test_workflows.json diff --git a/communities/microgalaxy/metadata/test_workflow_status.tsv b/communities/microgalaxy/metadata/test_workflow_status.tsv new file mode 100644 index 00000000..828a12e5 --- /dev/null +++ b/communities/microgalaxy/metadata/test_workflow_status.tsv @@ -0,0 +1,12 @@ +Link Name Source Projects Creators Creation time Update time To keep Deprecated +https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Halophiles workup of Comparative gene analysis https://usegalaxy.eu Anton Nekrutenko 2024-12-03 2024-12-05 True False +https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 pAllori Blood RNA https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-07-02 2024-11-24 True False +https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Metaproteomics workflow https://usegalaxy.eu Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Feature-Count Table Normalization https://usegalaxy.eu Johannes Effenberger 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 metaQuantome_datacreation_workflow https://usegalaxy.eu Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 metaquantome-function-worklow https://usegalaxy.eu Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-06-30 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Metatranscriptomics data analysis https://usegalaxy.eu Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False diff --git a/communities/microgalaxy/resources/test_curated_workflows.tsv b/communities/microgalaxy/resources/test_curated_workflows.tsv new file mode 100644 index 00000000..704eea93 --- /dev/null +++ b/communities/microgalaxy/resources/test_curated_workflows.tsv @@ -0,0 +1,12 @@ +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT True False +Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT True False diff --git a/communities/microgalaxy/resources/test_workflows.json b/communities/microgalaxy/resources/test_workflows.json new file mode 100644 index 00000000..4b3cfff6 --- /dev/null +++ b/communities/microgalaxy/resources/test_workflows.json @@ -0,0 +1,434 @@ +[ + { + "create_time": "2024-12-03", + "creators": [ + "Anton Nekrutenko" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "a2c46deea34d9d80", + "keep": true, + "latest_version": 2, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80", + "name": "Halophiles workup of Comparative gene analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "genome-annotation", + "name:microgalaxy" + ], + "tools": [ + "Filter1", + "join1", + "tab2fasta", + "Add_a_column1", + "bg_diamond_view", + "gops_intersect_1", + "collapse_dataset", + "rbc_mafft", + "rapidnj", + "bg_diamond", + "Cut1", + "cat1", + "regexColumn1", + "tp_split_on_column" + ], + "update_time": "2024-12-05", + "versions": 2 + }, + { + "create_time": "2023-07-02", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "ca9d3233b0912765", + "keep": true, + "latest_version": 43, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765", + "name": "pAllori Blood RNA", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:pallori", + "name:bloodrna", + "name:umi", + "name:barcode", + "name:transcriptomics" + ], + "tools": [ + "umi_tools_extract", + "__FILTER_FAILED_DATASETS__", + "collection_column_join", + "rna_star", + "featurecounts", + "multiqc", + "fastqc" + ], + "update_time": "2024-11-24", + "versions": 43 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Timothy Griffin", + "Pratik Jagtap", + "James Johnson", + "Clemens Blank", + "Subina Mehta" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "cefc49c13ff73231", + "keep": true, + "latest_version": 40, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231", + "name": "Metaproteomics workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:metaproteomics", + "name:galaxyp", + "name:massspectrometry", + "name:microgalaxy" + ], + "tools": [ + "search_gui", + "peptide_shaker", + "sqlite_to_tabular", + "query_tabular", + "unipept" + ], + "update_time": "2024-11-21", + "versions": 40 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Johannes Effenberger" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "6239178d7cc4ac68", + "keep": true, + "latest_version": 5, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68", + "name": "Feature-Count Table Normalization", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "normalization", + "softmax", + "relative-abundance", + "sigmoid", + "css", + "limma-tmm", + "limma-rle" + ], + "tools": [ + "map_param_value", + "__FILTER_EMPTY_DATASETS__", + "__BUILD_LIST__", + "__EXTRACT_DATASET__", + "Grep1" + ], + "update_time": "2024-11-21", + "versions": 5 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Metha", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "cd675ab32d3e7833", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833", + "name": "metaQuantome_datacreation_workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "Filter1", + "tp_replace_in_column", + "search_gui", + "peptide_shaker", + "tp_replace_in_line", + "flashlfq", + "query_tabular", + "msconvert", + "Remove beginning1", + "Cut1", + "regex1", + "unipept" + ], + "update_time": "2024-11-21", + "versions": 1 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Mehta", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane", + "Praveen Kumar" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "e5a89ef7b5f1c1d9", + "keep": true, + "latest_version": 3, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9", + "name": "metaquantome-function-worklow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "metaquantome_stat", + "metaquantome_db", + "metaquantome_viz", + "metaquantome_sample", + "metaquantome_filter", + "metaquantome_expand" + ], + "update_time": "2024-11-21", + "versions": 3 + }, + { + "create_time": "2023-06-30", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "466bdd8ba7b67264", + "keep": true, + "latest_version": 70, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "name": "pAllori Amplicon 16S Pre-Processing and Taxonomy Classification", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:16s", + "name:metagenomics", + "name:pallori" + ], + "tools": [ + "krakentools_kreport2krona", + "unzip", + "trimmomatic", + "ampvis2_load", + "taxonomy_krona_chart", + "ampvis2_heatmap", + "collection_column_join", + "lotus2", + "tp_cut_tool", + "__FLATTEN__", + "kraken2", + "ampvis2_ordinate", + "multiqc", + "fastqc", + "cutadapt" + ], + "update_time": "2024-11-21", + "versions": 70 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr ", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "c09159d7aad0f264", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264", + "name": "Cloud Aerosol MT-MG Contamination Filtering", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "filter_tabular", + "fastq_to_tabular", + "kraken2", + "seq_filter_by_id", + "recentrifuge", + "bowtie2" + ], + "update_time": "2024-11-21", + "versions": 2 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Valerie C. Schiml", + "Magnus \u00d8. Arntzen", + "Francesco Delogu", + "Praveen Kumar", + "Benoit Kunath", + "B\u00e9r\u00e9nice Batut", + " Subina Mehta", + "James E. Johnson", + " Bj\u00f6rn Gr\u00fcning", + "Phillip B. Pope", + "Pratik D. Jagtap", + "Timothy J. Griffin" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "fd90652d475ed739", + "keep": true, + "latest_version": 5, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", + "name": "Metatranscriptomics data analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "metatranscriptomics", + "microbiome" + ], + "tools": [ + "__UNZIP_COLLECTION__", + "bg_sortmerna", + "collection_column_join", + "kallisto_quant", + "fastqc", + "trim_galore" + ], + "update_time": "2024-11-21", + "versions": 5 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "63478edcea3f449a", + "keep": true, + "latest_version": 4, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=63478edcea3f449a", + "name": " Cloud-Aerosole MT-MG Functional Profiling", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "multiqc", + "featurecounts", + "bowtie2" + ], + "update_time": "2024-11-21", + "versions": 4 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "1ef76b7b86e15792", + "keep": true, + "latest_version": 6, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792", + "name": "Cloud-Aerosole MT-MG Pre-Processing", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "trimmomatic", + "multiqc", + "fastqc" + ], + "update_time": "2024-11-21", + "versions": 6 + } +] \ No newline at end of file diff --git a/communities/microgalaxy/resources/test_workflows.tsv b/communities/microgalaxy/resources/test_workflows.tsv index 5e61dade..704eea93 100644 --- a/communities/microgalaxy/resources/test_workflows.tsv +++ b/communities/microgalaxy/resources/test_workflows.tsv @@ -1,12 +1,12 @@ -Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI -Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column -pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT -Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT -Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT -metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT -metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT -pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT -Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT True False +Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT True False diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index 9bb85ed9..931eb371 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -408,7 +408,10 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List tags = shared.load_yaml(args.tags) # get status if file provided if args.status: - status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + try: + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + except Exception as ex: + status = {} else: status = {} wfs.filter_workflows_by_tags(tags, status) diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh index 92b52430..52785cb8 100644 --- a/sources/bin/get_community_workflows.sh +++ b/sources/bin/get_community_workflows.sh @@ -5,14 +5,16 @@ then python sources/bin/extract_galaxy_workflows.py \ filter \ --all "communities/all/resources/test_workflows.json" \ - --filtered "communities/microgalaxy/resources/test_workflows.tsv" \ - --tags "communities/microgalaxy/metadata/workflow_tags" - - python sources/bin/create_interactive_table.py \ - --input "communities/microgalaxy/resources/test_workflows.tsv" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/microgalaxy/resources/workflows.html" + --filtered "communities/microgalaxy/resources/test_workflows.json" \ + --tsv-filtered "communities/microgalaxy/resources/test_workflows.tsv" \ + --tags "communities/microgalaxy/metadata/workflow_tags" \ + --status "communities/microgalaxy/metadata/test_workflow_status.tsv" + python sources/bin/extract_galaxy_workflows.py \ + curate \ + --filtered "communities/microgalaxy/resources/test_workflows.json" \ + --status "communities/microgalaxy/metadata/test_workflow_status.tsv" \ + --curated "communities/microgalaxy/resources/test_curated_workflows.tsv" else for com_data_fp in communities/* ; do if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then