diff --git a/results/microgalaxy/tutorials.tsv b/results/microgalaxy/tutorials.tsv index edb30a10..837d094c 100644 --- a/results/microgalaxy/tutorials.tsv +++ b/results/microgalaxy/tutorials.tsv @@ -1,48 +1,48 @@ Topic Title Link EDAM topic EDAM operation Creation Last modification Version Tutorial Slides Video Workflows Tools Servers with precise tool versions Servers with tool but different versions Feedback number Feedback mean note Visitors Page views Visit duration Video views -Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence visualisation, Sequence alignment, Mapping, Genome visualisation, Read mapping 2018-06-14 2024-03-11 86 True False False True tp_grep_tool, circos_aln_to_links, bedtools_complementbed, collapse_dataset, circos_interval_to_tiles, fasta_compute_length, Grep1, tp_replace_in_column, tp_sed_tool, addValue, fasta_filter_by_length, bedtools_sortbed, lastz_wrapper_2, tp_sort_header_tool, random_lines1, Cut1, bedtools_intersectbed, tp_cat, mergeCols1, cat1, circos, tp_replace_in_line, datamash_ops, Filter1, jbrowse, upload1, join1 1 2.0 0 0 0.0 0 -Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Data handling, Visualisation, Sequencing quality control, Sequence alignment analysis, Sequence trimming, Read pre-processing, Sequence assembly validation, Primer removal, Sequence file editing, Local alignment, Variant calling, Sequence assembly visualisation, Read mapping, Statistical calculation, Sequence composition calculation, Formatting, Genome assembly, Sequence contamination filtering 2024-06-20 2024-06-20 0 True False False True coverm_contig, tp_cat, bandage_info, megahit_contig2fastg, megahit, collection_column_join, bg_uniq, bamtools, seqtk_subseq, filter_tabular, cutadapt, fastqc, bandage_image, bowtie2, random_lines1, quast, metaspades, ngsutils_bam_filter UseGalaxy.cz, UseGalaxy.eu 0 0 0 0.0 0 -Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Statistical calculation, Visualisation, Sequencing quality control, Sequence assembly validation, Sequence composition calculation, Genome assembly, Sequence assembly visualisation, Sequence contamination filtering 2021-03-24 2024-03-11 28 True False False True fastp, upload1, fastqc, shovill, bandage_image, bandage_info, quast UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no 8 4.5 0 0 0.0 0 -Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance Box-Whisker plot plotting, Scatter plot plotting, Visualisation, Sequencing error detection, Sequencing quality control, Sequence alignment, Cross-assembly, Sequence assembly validation, Sequence composition calculation, De-novo assembly, Sequence assembly visualisation, Mapping assembly, Read mapping, Statistical calculation, Filtering, Genome assembly, Sequence contamination filtering 2021-03-24 2024-03-13 35 True False False True filtlong, CONVERTER_bz2_to_uncompressed, fastp, upload1, fastqc, bandage_image, bwa_mem2, flye, quast, nanoplot, porechop, polypolish UseGalaxy.eu UseGalaxy.cz 2 4.0 0 0 0.0 0 -Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Coding region prediction, Genome annotation, Validation, Statistical calculation, Visualisation, Sequencing quality control, Aggregation, Gene prediction, Sequence composition calculation, Genome assembly, Sequence assembly validation 2017-10-11 2024-03-11 61 True True False True unicycler, multiqc, fastqc, prokka, quast UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 8 3.75 0 0 0.0 0 -Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification 2024-03-04 2024-04-04 5 True False False True recentrifuge, est_abundance, kraken2, upload1 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 1 5.0 0 0 0.0 0 -Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2023-02-15 19 True False False True upload1, interactive_tool_rstudio, raxml UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 6 4.333333333333333 0 0 0.0 0 -Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2022-03-16 2024-03-12 15 True False False True snippy, tp_cat, snp_dists, tp_grep_tool, tb_variant_filter, bcftools_consensus, upload1, tp_easyjoin_tool, snp_sites, tb_profiler_profile, addName, collapse_dataset, trimmomatic, samtools_view, Grep1, tp_replace_in_line, __MERGE_COLLECTION__, tp_sed_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 7 4.0 0 0 0.0 0 -Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Coding region prediction, Genome annotation, Gene prediction, Genome visualisation 2018-03-06 2024-05-29 43 True True True True jbrowse, prokka UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 17 3.764705882352941 0 0 0.0 0 -Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Protein feature detection, Genome annotation, Scaffolding, Structural variation detection, Multilocus sequence typing, Nucleic acid feature detection, Genome assembly, Sequence motif recognition, Genome visualisation 2024-02-01 2024-03-13 8 True False False True Grouping1, isescan, jbrowse, tp_replace_in_column, integron_finder, plasmidfinder, upload1, bakta, tbl2gff3, tp_tail_tool Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 1 1.0 0 0 0.0 0 -Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Read mapping, Genome annotation, Genome visualisation 2024-01-23 2024-03-13 9 True False False True jbrowse, upload1, bakta, bowtie2, tbl2gff3, Grep1, staramr_search UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 0 0 0.0 0 -Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2024-05-29 40 True True True True jbrowse, list_organism, create_account, iframe, create_or_update UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 5 4.6 0 0 0.0 0 -Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny Coding region prediction, Database search, De-novo assembly, Transcriptome assembly, Multiple sequence alignment, Sequence alignment analysis, Phylogenetic tree generation 2022-09-08 2024-03-18 30 True False False True Add_a_column1, tp_split_on_column, Filter1, bg_diamond_makedb, bg_diamond_view, orfipy, cat1, regexColumn1, tab2fasta, collapse_dataset, gops_intersect_1, join1, bg_diamond, rapidnj, Cut1, rbc_mafft UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 0 0 0.0 0 -Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Primer removal, Read pre-processing, Transposon prediction, Sequence trimming 2019-07-02 2024-03-15 52 True True False True deeptools_bam_coverage, Add_a_column1, Filter1, gff_to_prot, __EXTRACT_DATASET__, cutadapt, bg_find_subsequences, bowtie_wrapper, tp_sort_header_tool, transit_gumbel, Cut1, tp_easyjoin_tool UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 4 4.5 0 0 0.0 0 -Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Coding region prediction, Genome annotation, Gene prediction, Genome visualisation 2018-03-06 2024-05-29 43 True True True True jbrowse, prokka UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 17 3.764705882352941 0 0 0.0 0 -Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2018-02-26 2024-03-14 36 True False False True snippy, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 12 4.416666666666667 0 0 0.0 0 -Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence visualisation, Sequence alignment, Mapping, Genome visualisation, Read mapping 2018-06-14 2024-03-11 86 True False False True tp_grep_tool, circos_aln_to_links, bedtools_complementbed, collapse_dataset, circos_interval_to_tiles, fasta_compute_length, Grep1, tp_replace_in_column, tp_sed_tool, addValue, fasta_filter_by_length, bedtools_sortbed, lastz_wrapper_2, tp_sort_header_tool, random_lines1, Cut1, bedtools_intersectbed, tp_cat, mergeCols1, cat1, circos, tp_replace_in_line, datamash_ops, Filter1, jbrowse, upload1, join1 1 2.0 0 0 0.0 0 -Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance Box-Whisker plot plotting, Scatter plot plotting, Visualisation, Sequencing error detection, Sequencing quality control, Sequence alignment, Cross-assembly, Sequence assembly validation, Sequence composition calculation, De-novo assembly, Sequence assembly visualisation, Mapping assembly, Read mapping, Statistical calculation, Filtering, Genome assembly, Sequence contamination filtering 2021-03-24 2024-03-13 35 True False False True filtlong, CONVERTER_bz2_to_uncompressed, fastp, upload1, fastqc, bandage_image, bwa_mem2, flye, quast, nanoplot, porechop, polypolish UseGalaxy.eu UseGalaxy.cz 2 4.0 0 0 0.0 0 -Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Protein feature detection, Genome annotation, Scaffolding, Structural variation detection, Multilocus sequence typing, Nucleic acid feature detection, Genome assembly, Sequence motif recognition, Genome visualisation 2024-02-01 2024-03-13 8 True False False True Grouping1, isescan, jbrowse, tp_replace_in_column, integron_finder, plasmidfinder, upload1, bakta, tbl2gff3, tp_tail_tool Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 1 1.0 0 0 0.0 0 -Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Read mapping, Genome annotation, Genome visualisation 2024-01-23 2024-03-13 9 True False False True jbrowse, upload1, bakta, bowtie2, tbl2gff3, Grep1, staramr_search UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 0 0 0.0 0 -Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2024-05-29 40 True True True True jbrowse, list_organism, create_account, iframe, create_or_update UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 5 4.6 0 0 0.0 0 -Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis DNA barcoding, Sequence clustering, Taxonomic classification, Sequence read processing, Visualisation, Sequencing quality control, Phylogenetic analysis 2017-06-22 2024-03-14 4 True False False True mothur_make_shared, mothur_classify_seqs, mothur_screen_seqs, mothur_align_seqs, mothur_cluster_split, humann2_regroup_table, metaphlan2krona, taxonomy_krona_chart, mothur_make_biom, mothur_unique_seqs, krona-text, humann2, mothur_classify_otu, mothur_filter_seqs, mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, metaphlan2, mothur_merge_files, humann2_renorm_table UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 16 4.0625 0 0 0.0 0 -Microbiome Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis Box-Whisker plot plotting, Validation, Multiple sequence alignment, Data handling, Antimicrobial resistance prediction, Phylogenetic tree reconstruction, Phylogenetic tree generation, Taxonomic classification, Scatter plot plotting, Visualisation, Sequence assembly, Sequencing quality control, Base-calling, Sequence alignment analysis, Cross-assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), De-novo assembly, Variant calling, Multilocus sequence typing, Sequence assembly visualisation, Mapping assembly, Statistical calculation, Aggregation, Pairwise sequence alignment, Phylogenetic tree analysis, Mapping, Phylogenetic tree generation (from molecular sequences), Sequence composition calculation, Genome assembly, Sequence contamination filtering 2023-01-26 2024-06-19 18 True False False True Paste1, tp_multijoin_tool, param_value_from_file, tp_head_tool, clustalw, ggplot2_heatmap, multiqc, collapse_dataset, tp_sorted_uniq, samtools_coverage, Count1, medaka_consensus_pipeline, Grep1, tp_replace_in_column, abricate, table_compute, Add_a_column1, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, __BUILD_LIST__, taxonomy_krona_chart, collection_column_join, __FILTER_EMPTY_DATASETS__, flye, fasta2tab, Cut1, samtools_depth, split_file_to_collection, mlst, clair3, barchart_gnuplot, tp_split_on_column, Grouping1, krakentools_extract_kraken_reads, add_line_to_file, collection_element_identifiers, tp_cut_tool, fastp, regexColumn1, krakentools_kreport2krona, minimap2, fastqc, bamtools_split_mapped, newick_display, bandage_image, snpSift_filter, bedtools_getfastabed, CONVERTER_gz_to_uncompressed, kraken2, snpSift_extractFields, bcftools_norm, compose_text_param, fasttree, porechop, bcftools_consensus, tab2fasta, regex1, samtools_fastx, tp_find_and_replace, nanoplot, __FILTER_FAILED_DATASETS__ UseGalaxy.eu 1 5.0 0 0 0.0 0 -Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Visualisation, Aggregation, Phylogenetic tree analysis, Nucleic acid sequence analysis, Taxonomic classification 2023-05-03 2024-05-29 4 True False False True est_abundance, kraken2, interactive_tool_phinch, metaphlan, taxonomy_krona_chart, __UNZIP_COLLECTION__, krakentools_kreport2krona, kraken_biom, interactive_tool_pavian UseGalaxy.eu UseGalaxy.org.au 3 4.333333333333333 0 0 0.0 0 -Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Data handling, Visualisation, Sequencing quality control, Sequence alignment analysis, Sequence trimming, Read pre-processing, Sequence assembly validation, Primer removal, Sequence file editing, Local alignment, Variant calling, Sequence assembly visualisation, Read mapping, Statistical calculation, Sequence composition calculation, Formatting, Genome assembly, Sequence contamination filtering 2022-12-05 2024-05-29 4 True False False True coverm_contig, tp_cat, bandage_info, megahit_contig2fastg, megahit, collection_column_join, bg_uniq, bamtools, seqtk_subseq, filter_tabular, cutadapt, fastqc, bandage_image, bowtie2, random_lines1, quast, metaspades, ngsutils_bam_filter UseGalaxy.cz, UseGalaxy.eu 0 0 0 0.0 0 -Microbiome Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance Box-Whisker plot plotting, Sequence analysis, De-novo assembly, Sequence assembly visualisation, Mapping assembly, Scatter plot plotting, Aggregation, Pairwise sequence alignment, Genome assembly 2019-06-25 2024-05-29 4 True False False True nanoplot, unicycler, PlasFlow, minimap2, bandage_image, racon, miniasm, gfa_to_fa, staramr_search UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 10 5.0 0 0 0.0 0 -Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis Visualisation, Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Taxonomic classification, Sequence contamination filtering 2020-11-24 2024-03-21 4 True False False True kraken2, Remove beginning1, taxonomy_krona_chart, fastp, multiqc, datamash_reverse, fastqc, tp_replace_in_line, porechop UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 13 4.6923076923076925 0 0 0.0 0 -Microbiome Metatranscriptomics analysis using microbiome RNA-seq data https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Validation, Taxonomic classification, Sequence comparison, Visualisation, Sequencing quality control, Phylogenetic tree editing, Phylogenetic inference, Sequence alignment analysis, Phylogenetic analysis, Read pre-processing, Sequence trimming, Primer removal, Sequence similarity search, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree analysis, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic tree visualisation 2019-11-21 2024-05-29 4 True True False True humann_regroup_table, export2graphlan, multiqc, cutadapt, Grep1, bg_sortmerna, taxonomy_krona_chart, fastq_paired_end_interlacer, humann, humann_renorm_table, Cut1, graphlan, metaphlan, humann_rename_table, humann_unpack_pathways, fastqc, humann_split_stratified_table, combine_metaphlan2_humann2, graphlan_annotate, tp_find_and_replace UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 6 4.5 0 0 0.0 0 -Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Validation, Taxonomic classification, Sequence comparison, Visualisation, Sequencing quality control, Phylogenetic tree editing, Phylogenetic inference, Sequence alignment analysis, Phylogenetic analysis, Read pre-processing, Sequence trimming, Primer removal, Sequence similarity search, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree analysis, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic tree visualisation 2020-02-13 2024-05-29 4 True False False True humann_regroup_table, export2graphlan, multiqc, cutadapt, Grep1, bg_sortmerna, taxonomy_krona_chart, fastq_paired_end_interlacer, humann, humann_renorm_table, Cut1, graphlan, metaphlan, humann_rename_table, humann_unpack_pathways, fastqc, humann_split_stratified_table, combine_metaphlan2_humann2, graphlan_annotate, tp_find_and_replace UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 1 5.0 0 0 0.0 0 -Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Statistical calculation, Sequencing quality control, Aggregation, Sequence composition calculation, Taxonomic classification, Sequence contamination filtering 2022-09-29 2024-05-29 4 True False False True kraken2, Filter1, taxonomy_krona_chart, fastp, krakentools_kreport2krona, fastqc, porechop GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 3 4.666666666666667 0 0 0.0 0 -Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis DNA barcoding, Deposition, Visualisation, Analysis, Variant calling 2024-06-05 2024-06-17 9 True False False True dada2_seqCounts, tp_head_tool, dada2_mergePairs, __SORTLIST__, tp_replace_in_column, Add_a_column1, phyloseq_from_dada2, __UNZIP_COLLECTION__, interactive_tool_phyloseq, Grouping1, dada2_makeSequenceTable, cat1, collection_element_identifiers, dada2_filterAndTrim, tp_replace_in_line, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_dada, dada2_plotQualityProfile, dada2_learnErrors UseGalaxy.eu, UseGalaxy.fr 0 0 0 0.0 0 -Microbiome QIIME 2 Cancer Microbiome Intervention https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html Microbial ecology, Taxonomy, Sequence analysis 2024-02-12 2024-03-14 6 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 1 5.0 0 0 0.0 0 -Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Genome assembly, Sequence assembly validation 2023-12-05 2024-03-14 4 True False False False megahit, checkm_lineage_wf GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 0 0 0.0 0 -Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis 2024-03-14 2024-03-14 2 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 1 5.0 0 0 0.0 0 -Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction, Taxonomic classification, Phylogenetic tree generation, Sequence read processing, Visualisation, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis 2019-05-13 2024-05-31 7 True False False True mothur_make_shared, mothur_summary_single, mothur_remove_groups, mothur_classify_seqs, mothur_screen_seqs, collapse_dataset, mothur_heatmap_sim, mothur_cluster_split, mothur_sub_sample, mothur_unique_seqs, mothur_dist_shared, mothur_classify_otu, mothur_venn, newick_display, mothur_dist_seqs, XY_Plot_1, mothur_remove_seqs, mothur_tree_shared, mothur_filter_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_remove_lineage, mothur_chimera_vsearch, mothur_summary_seqs, mothur_count_seqs, mothur_cluster, mothur_count_groups UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 9 4.666666666666667 0 0 0.0 0 -Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction, Taxonomic classification, Phylogenetic tree generation, Sequence read processing, Visualisation, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic analysis 2017-02-12 2024-03-14 4 True False False True mothur_make_shared, mothur_summary_single, mothur_remove_groups, mothur_classify_seqs, mothur_screen_seqs, mothur_seq_error, mothur_heatmap_sim, mothur_align_seqs, mothur_cluster_split, mothur_sub_sample, taxonomy_krona_chart, mothur_make_biom, mothur_unique_seqs, mothur_dist_shared, mothur_classify_otu, mothur_venn, newick_display, mothur_dist_seqs, XY_Plot_1, mothur_remove_seqs, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_filter_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_remove_lineage, mothur_make_contigs, mothur_chimera_vsearch, mothur_summary_seqs, mothur_get_groups, mothur_count_seqs, mothur_cluster, mothur_count_groups UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 44 4.613636363636363 0 0 0.0 0 -Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Sequence analysis, Validation, Genome visualisation, Antimicrobial resistance prediction, Local alignment, Variant calling, Phylogenetic tree generation, Taxonomic classification, Statistical calculation, Sequencing quality control, Sequence alignment, Global alignment, Sequence composition calculation, Sequence alignment analysis, Phylogenetic tree visualisation, Sequence contamination filtering 2020-07-25 2024-06-12 75 True False False True tbvcfreport, multiqc, tp_sed_tool, qualimap_bamqc, tb_profiler_profile, EMBOSS:%20seqret84, snippy, fastp, fastqc, mosdepth, samtools_stats, tp_awk_tool, kraken2, jbrowse, tb_variant_filter, bcftools_consensus, upload1, EMBOSS: seqret84, __FLATTEN__, jvarkit_wgscoverageplotter 25 4.64 0 0 0.0 0 -Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Read mapping, Genome annotation, Genome visualisation 2024-01-23 2024-03-13 9 True False False True jbrowse, upload1, bakta, bowtie2, tbl2gff3, Grep1, staramr_search UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 0 0 0.0 0 -Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2023-02-15 19 True False False True upload1, interactive_tool_rstudio, raxml UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 6 4.333333333333333 0 0 0.0 0 -Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2022-03-16 2024-03-12 15 True False False True snippy, tp_cat, snp_dists, tp_grep_tool, tb_variant_filter, bcftools_consensus, upload1, tp_easyjoin_tool, snp_sites, tb_profiler_profile, addName, collapse_dataset, trimmomatic, samtools_view, Grep1, tp_replace_in_line, __MERGE_COLLECTION__, tp_sed_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 7 4.0 0 0 0.0 0 -Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Statistical inference, Differential protein expression analysis, Visualisation, Principal component visualisation, Quantification, Functional clustering, Heat map generation, Indexing, Filtering, Query and retrieval 2020-10-29 2024-03-14 36 True False False True metaquantome_filter, metaquantome_stat, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 0 0 0.0 0 -Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Prediction and recognition 2017-06-28 2024-05-29 57 True False False True sqlite_to_tabular, query_tabular, peptide_shaker, unipept, search_gui UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 1 5.0 0 0 0.0 0 -Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Prediction and recognition, Filtering, Formatting, Label-free quantification 2020-10-16 2024-03-14 90 True False False True flashlfq, Remove beginning1, Filter1, query_tabular, regex1, peptide_shaker, unipept, msconvert, Grep1, Cut1, tp_replace_in_line, tp_replace_in_column, search_gui UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 0 0 0.0 0 -Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Statistical inference, Differential protein expression analysis, Visualisation, Principal component visualisation, Quantification, Functional clustering, Heat map generation, Indexing, Filtering, Query and retrieval 2020-10-29 2024-03-14 38 True False False True metaquantome_filter, metaquantome_stat, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 0 0 0.0 0 -Variant Analysis Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Generation, Data handling, Variant calling, Genome indexing, Read mapping, Statistical calculation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Sequence alignment analysis, Formatting 2017-02-16 2024-03-14 39 True False False True bwa_mem, vcffilter2, bamleftalign, freebayes, bamFilter, vcf2tsv, fastqc, picard_MarkDuplicates, Cut1, picard_MergeSamFiles UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 3 2.3333333333333335 0 0 0.0 0 -Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Sequence analysis, Validation, Genome visualisation, Antimicrobial resistance prediction, Local alignment, Variant calling, Phylogenetic tree generation, Taxonomic classification, Statistical calculation, Sequencing quality control, Sequence alignment, Global alignment, Sequence composition calculation, Sequence alignment analysis, Phylogenetic tree visualisation, Sequence contamination filtering 2020-07-25 2024-06-12 75 True False False True tbvcfreport, multiqc, tp_sed_tool, qualimap_bamqc, tb_profiler_profile, EMBOSS:%20seqret84, snippy, fastp, fastqc, mosdepth, samtools_stats, tp_awk_tool, kraken2, jbrowse, tb_variant_filter, bcftools_consensus, upload1, EMBOSS: seqret84, __FLATTEN__, jvarkit_wgscoverageplotter 25 4.64 0 0 0.0 0 -Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2018-02-26 2024-03-14 36 True False False True snippy, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 12 4.416666666666667 0 0 0.0 0 +Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Genome visualisation, Sequence alignment, Read mapping, Sequence visualisation, Mapping 2018-06-14 2024-03-11 86 True False False True Cut1, tp_replace_in_line, mergeCols1, tp_replace_in_column, fasta_filter_by_length, Grep1, cat1, circos_aln_to_links, jbrowse, fasta_compute_length, collapse_dataset, random_lines1, bedtools_sortbed, lastz_wrapper_2, addValue, circos, join1, Filter1, bedtools_intersectbed, bedtools_complementbed, upload1, tp_sed_tool, tp_cat, datamash_ops, tp_sort_header_tool, circos_interval_to_tiles, tp_grep_tool 1 2.0 5828 11935 3.033333333333333 0 +Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence composition calculation, Genome assembly, Visualisation, Primer removal, Sequence assembly visualisation, Sequence file editing, Read mapping, Statistical calculation, Data handling, Sequence contamination filtering, Local alignment, Sequence alignment analysis, Variant calling, Sequencing quality control, Read pre-processing, Sequence assembly validation, Formatting, Sequence trimming 2024-06-24 2024-06-24 0 True False False True filter_tabular, bandage_image, metaspades, megahit, quast, cutadapt, tp_cat, ngsutils_bam_filter, megahit_contig2fastg, random_lines1, bamtools, bowtie2, bandage_info, collection_column_join, coverm_contig, seqtk_subseq, fastqc, bg_uniq UseGalaxy.cz, UseGalaxy.eu 0 1 1 0.0 0 +Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Sequence assembly visualisation, Sequence composition calculation, Sequence contamination filtering, Genome assembly, Statistical calculation, Sequencing quality control, Visualisation, Sequence assembly validation 2021-03-24 2024-03-11 28 True False False True bandage_image, upload1, quast, bandage_info, fastqc, fastp, shovill UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no 8 4.5 6115 9890 3.7333333333333334 0 +Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance De-novo assembly, Sequence composition calculation, Genome assembly, Sequencing error detection, Visualisation, Sequencing quality control, Mapping assembly, Sequence assembly visualisation, Sequence assembly validation, Cross-assembly, Box-Whisker plot plotting, Scatter plot plotting, Filtering, Read mapping, Statistical calculation, Sequence alignment, Sequence contamination filtering 2021-03-24 2024-03-13 35 True False False True flye, nanoplot, bandage_image, polypolish, upload1, quast, porechop, CONVERTER_bz2_to_uncompressed, bwa_mem2, filtlong, fastqc, fastp UseGalaxy.eu UseGalaxy.cz 2 4.0 6353 9777 3.4166666666666665 0 +Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Sequence composition calculation, Genome assembly, Validation, Coding region prediction, Sequencing quality control, Visualisation, Sequence assembly validation, Statistical calculation, Gene prediction, Aggregation, Genome annotation 2017-10-11 2024-03-11 61 True True False True quast, prokka, unicycler, multiqc, fastqc UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 8 3.75 1994916 5552489 4.566666666666666 0 +Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Cross-assembly, Taxonomic classification, Expression analysis 2024-03-04 2024-04-04 5 True False False True kraken2, recentrifuge, upload1, est_abundance UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 1 5.0 165 226 4.866666666666666 0 +Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2023-02-15 19 True False False True raxml, interactive_tool_rstudio, upload1 UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 6 4.333333333333333 1211 1857 2.2666666666666666 0 +Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2022-03-16 2024-03-12 15 True False False True snippy, tb_variant_filter, tp_replace_in_line, trimmomatic, bcftools_consensus, snp_sites, tp_sed_tool, addName, tp_cat, upload1, collapse_dataset, Grep1, __MERGE_COLLECTION__, tp_easyjoin_tool, tb_profiler_profile, samtools_view, tp_grep_tool, snp_dists UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 7 4.0 1377 2211 3.183333333333333 0 +Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome annotation, Coding region prediction, Gene prediction, Genome visualisation 2018-03-06 2024-05-29 43 True True True True prokka, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 17 3.764705882352941 1999341 5560175 4.316666666666666 0 +Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Structural variation detection, Genome assembly, Nucleic acid feature detection, Protein feature detection, Scaffolding, Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome annotation 2024-02-01 2024-03-13 8 True False False True tp_tail_tool, upload1, bakta, isescan, Grouping1, tp_replace_in_column, tbl2gff3, plasmidfinder, integron_finder, jbrowse Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 1 1.0 1237 1630 2.4833333333333334 0 +Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome annotation, Genome visualisation, Read mapping 2024-01-23 2024-03-13 9 True False False True upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 726 1061 3.066666666666667 0 +Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2024-05-29 40 True True True True iframe, create_or_update, list_organism, create_account, jbrowse UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 5 4.6 1757138 4755339 5.016666666666667 0 +Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction, Phylogenetic tree generation, Transcriptome assembly, Database search 2022-09-08 2024-03-18 30 True False False True Add_a_column1, gops_intersect_1, Cut1, orfipy, bg_diamond_view, tp_split_on_column, bg_diamond, tab2fasta, rbc_mafft, collapse_dataset, cat1, regexColumn1, join1, rapidnj, Filter1, bg_diamond_makedb UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 910 1395 3.1166666666666667 0 +Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Transposon prediction, Primer removal, Read pre-processing, Sequence trimming 2019-07-02 2024-03-15 52 True True False True Add_a_column1, Cut1, bowtie_wrapper, transit_gumbel, cutadapt, gff_to_prot, tp_sort_header_tool, __EXTRACT_DATASET__, deeptools_bam_coverage, tp_easyjoin_tool, bg_find_subsequences, Filter1 UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 4 4.5 1990676 5545573 4.25 0 +Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome annotation, Coding region prediction, Gene prediction, Genome visualisation 2018-03-06 2024-05-29 43 True True True True prokka, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 17 3.764705882352941 1999341 5560176 4.316666666666666 0 +Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2018-02-26 2024-03-14 36 True False False True snippy, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 12 4.416666666666667 11631 19648 1.9833333333333334 0 +Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Genome visualisation, Sequence alignment, Read mapping, Sequence visualisation, Mapping 2018-06-14 2024-03-11 86 True False False True Cut1, tp_replace_in_line, mergeCols1, tp_replace_in_column, fasta_filter_by_length, Grep1, cat1, circos_aln_to_links, jbrowse, fasta_compute_length, collapse_dataset, random_lines1, bedtools_sortbed, lastz_wrapper_2, addValue, circos, join1, Filter1, bedtools_intersectbed, bedtools_complementbed, upload1, tp_sed_tool, tp_cat, datamash_ops, tp_sort_header_tool, circos_interval_to_tiles, tp_grep_tool 1 2.0 5828 11935 3.033333333333333 0 +Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance De-novo assembly, Sequence composition calculation, Genome assembly, Sequencing error detection, Visualisation, Sequencing quality control, Mapping assembly, Sequence assembly visualisation, Sequence assembly validation, Cross-assembly, Box-Whisker plot plotting, Scatter plot plotting, Filtering, Read mapping, Statistical calculation, Sequence alignment, Sequence contamination filtering 2021-03-24 2024-03-13 35 True False False True flye, nanoplot, bandage_image, polypolish, upload1, quast, porechop, CONVERTER_bz2_to_uncompressed, bwa_mem2, filtlong, fastqc, fastp UseGalaxy.eu UseGalaxy.cz 2 4.0 6353 9777 3.4166666666666665 0 +Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Structural variation detection, Genome assembly, Nucleic acid feature detection, Protein feature detection, Scaffolding, Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome annotation 2024-02-01 2024-03-13 8 True False False True tp_tail_tool, upload1, bakta, isescan, Grouping1, tp_replace_in_column, tbl2gff3, plasmidfinder, integron_finder, jbrowse Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 1 1.0 1237 1630 2.4833333333333334 0 +Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome annotation, Genome visualisation, Read mapping 2024-01-23 2024-03-13 9 True False False True upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 726 1061 3.066666666666667 0 +Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2024-05-29 40 True True True True iframe, create_or_update, list_organism, create_account, jbrowse UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 5 4.6 1757138 4755340 5.016666666666667 0 +Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Sequence read processing, Sequencing quality control, Visualisation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering 2017-06-22 2024-03-14 4 True False False True mothur_summary_seqs, mothur_classify_seqs, humann2_regroup_table, krona-text, mothur_pre_cluster, mothur_align_seqs, mothur_make_group, mothur_unique_seqs, humann2_renorm_table, metaphlan2, metaphlan2krona, mothur_merge_files, mothur_make_biom, mothur_make_shared, mothur_screen_seqs, mothur_count_seqs, mothur_cluster_split, mothur_classify_otu, mothur_filter_seqs, taxonomy_krona_chart, humann2 UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 16 4.0625 2225 2984 2.65 0 +Microbiome Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis Phylogenetic tree reconstruction, Sequence composition calculation, Base-calling, Genome assembly, Phylogenetic tree generation (from molecular sequences), Validation, Visualisation, Sequence assembly visualisation, Multilocus sequence typing, Scatter plot plotting, Statistical calculation, Data handling, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Pairwise sequence alignment, Sequence contamination filtering, De-novo assembly, Sequence alignment analysis, Variant calling, Mapping, Sequencing quality control, Phylogenetic tree generation, Mapping assembly, Box-Whisker plot plotting, Cross-assembly, Taxonomic classification, Antimicrobial resistance prediction, Multiple sequence alignment, Sequence assembly, Aggregation, Phylogenetic tree analysis 2023-01-26 2024-06-19 18 True False False True nanoplot, bandage_image, Cut1, CONVERTER_gz_to_uncompressed, bcftools_consensus, samtools_fastx, Grouping1, tp_replace_in_column, Grep1, __BUILD_LIST__, tp_find_and_replace, regex1, clustalw, fastp, tp_sorted_uniq, collection_element_identifiers, Paste1, flye, Add_a_column1, medaka_consensus_pipeline, Count1, minimap2, table_compute, tp_split_on_column, bamtools_split_mapped, clair3, kraken2, collapse_dataset, __FILTER_EMPTY_DATASETS__, compose_text_param, samtools_depth, snpSift_extractFields, regexColumn1, fastqc, abricate, newick_display, krakentools_extract_kraken_reads, bcftools_norm, barchart_gnuplot, Remove beginning1, samtools_coverage, split_file_to_collection, porechop, tp_multijoin_tool, mlst, tp_head_tool, multiqc, collection_column_join, fasta_merge_files_and_filter_unique_sequences, param_value_from_file, add_line_to_file, krakentools_kreport2krona, bedtools_getfastabed, fasttree, tab2fasta, ggplot2_heatmap, snpSift_filter, __FILTER_FAILED_DATASETS__, taxonomy_krona_chart, fasta2tab, tp_cut_tool UseGalaxy.eu 1 5.0 1259 1884 2.8 0 +Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Taxonomic classification, Aggregation, Nucleic acid sequence analysis, Statistical calculation, Visualisation, Phylogenetic tree analysis 2023-05-03 2024-05-29 4 True False False True interactive_tool_pavian, interactive_tool_phinch, est_abundance, kraken2, metaphlan, kraken_biom, taxonomy_krona_chart, __UNZIP_COLLECTION__, krakentools_kreport2krona UseGalaxy.eu UseGalaxy.org.au 3 4.333333333333333 2673 3680 1.9 0 +Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence composition calculation, Genome assembly, Visualisation, Primer removal, Sequence assembly visualisation, Sequence file editing, Read mapping, Statistical calculation, Data handling, Sequence contamination filtering, Local alignment, Sequence alignment analysis, Variant calling, Sequencing quality control, Read pre-processing, Sequence assembly validation, Formatting, Sequence trimming 2022-12-05 2024-05-29 4 True False False True filter_tabular, bandage_image, metaspades, megahit, quast, cutadapt, tp_cat, ngsutils_bam_filter, megahit_contig2fastg, random_lines1, bamtools, bowtie2, bandage_info, collection_column_join, coverm_contig, seqtk_subseq, fastqc, bg_uniq UseGalaxy.cz, UseGalaxy.eu 0 1100 1543 2.6 0 +Microbiome Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance De-novo assembly, Genome assembly, Mapping assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Scatter plot plotting, Aggregation, Sequence analysis, Pairwise sequence alignment 2019-06-25 2024-05-29 4 True False False True nanoplot, bandage_image, racon, staramr_search, PlasFlow, gfa_to_fa, unicycler, miniasm, minimap2 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 10 5.0 902 1419 4.05 0 +Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis Taxonomic classification, Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control, Visualisation, Sequence contamination filtering 2020-11-24 2024-03-21 4 True False False True tp_replace_in_line, kraken2, Remove beginning1, porechop, multiqc, datamash_reverse, taxonomy_krona_chart, fastqc, fastp UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 13 4.6923076923076925 1835 2617 2.9 0 +Microbiome Metatranscriptomics analysis using microbiome RNA-seq data https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence composition calculation, Phylogenetic tree visualisation, Validation, Phylogenetic inference, Primer removal, Visualisation, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control, Read pre-processing, Phylogenetic tree editing, Taxonomic classification, Conversion, Nucleic acid sequence analysis, Phylogenetic tree analysis, Sequence trimming 2019-11-21 2024-05-29 4 True True False True graphlan_annotate, Cut1, humann_split_stratified_table, bg_sortmerna, Grep1, tp_find_and_replace, graphlan, humann_renorm_table, humann, metaphlan, humann_rename_table, fastqc, multiqc, combine_metaphlan2_humann2, fastq_paired_end_interlacer, cutadapt, export2graphlan, humann_regroup_table, taxonomy_krona_chart, humann_unpack_pathways UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 6 4.5 1986067 5535600 4.3 0 +Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence composition calculation, Phylogenetic tree visualisation, Validation, Phylogenetic inference, Primer removal, Visualisation, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control, Read pre-processing, Phylogenetic tree editing, Taxonomic classification, Conversion, Nucleic acid sequence analysis, Phylogenetic tree analysis, Sequence trimming 2020-02-13 2024-05-29 4 True False False True graphlan_annotate, Cut1, humann_split_stratified_table, bg_sortmerna, Grep1, tp_find_and_replace, graphlan, humann_renorm_table, humann, metaphlan, humann_rename_table, fastqc, multiqc, combine_metaphlan2_humann2, fastq_paired_end_interlacer, cutadapt, export2graphlan, humann_regroup_table, taxonomy_krona_chart, humann_unpack_pathways UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 1 5.0 184 236 2.0 0 +Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Taxonomic classification, Sequence composition calculation, Aggregation, Statistical calculation, Sequencing quality control, Visualisation, Sequence contamination filtering 2022-09-29 2024-05-29 4 True False False True kraken2, porechop, taxonomy_krona_chart, fastqc, fastp, Filter1, krakentools_kreport2krona GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 3 4.666666666666667 969 1570 3.0 0 +Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis Variant calling, DNA barcoding, Deposition, Visualisation, Analysis 2024-06-05 2024-06-17 9 True False False True tp_replace_in_line, dada2_filterAndTrim, dada2_plotQualityProfile, Grouping1, tp_replace_in_column, cat1, interactive_tool_phyloseq, collection_element_identifiers, Add_a_column1, dada2_mergePairs, dada2_seqCounts, __UNZIP_COLLECTION__, __SORTLIST__, dada2_dada, dada2_makeSequenceTable, phyloseq_from_dada2, tp_head_tool, dada2_removeBimeraDenovo, dada2_learnErrors, dada2_assignTaxonomyAddspecies UseGalaxy.eu, UseGalaxy.fr 0 104 129 1.4833333333333334 0 +Microbiome QIIME 2 Cancer Microbiome Intervention https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html Microbial ecology, Taxonomy, Sequence analysis 2024-02-12 2024-03-14 6 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 1 5.0 83 152 1.2333333333333334 0 +Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Sequence composition calculation, Genome assembly, Statistical calculation, Validation, Sequencing quality control, Sequence assembly validation 2023-12-05 2024-03-14 4 True False False False checkm_lineage_wf, megahit GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 1134 1367 1.5166666666666666 0 +Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis 2024-03-14 2024-03-14 2 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 1 5.0 72 94 3.4166666666666665 0 +Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Visualisation, Phylogenetic tree generation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering, Phylogenetic tree analysis 2019-05-13 2024-05-31 7 True False False True mothur_summary_seqs, mothur_classify_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_remove_lineage, mothur_unique_seqs, collapse_dataset, XY_Plot_1, newick_display, mothur_sub_sample, mothur_summary_single, mothur_venn, mothur_make_shared, mothur_heatmap_sim, mothur_dist_shared, mothur_screen_seqs, mothur_count_seqs, mothur_cluster_split, mothur_remove_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_remove_groups, mothur_cluster, mothur_count_groups, mothur_dist_seqs, mothur_chimera_vsearch, mothur_tree_shared UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 9 4.666666666666667 1485 2824 6.05 0 +Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Visualisation, Phylogenetic tree generation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering, Phylogenetic tree analysis 2017-02-12 2024-03-14 4 True False False True mothur_make_contigs, mothur_seq_error, mothur_summary_seqs, mothur_classify_seqs, mothur_pre_cluster, mothur_align_seqs, mothur_rarefaction_single, mothur_remove_lineage, mothur_unique_seqs, mothur_taxonomy_to_krona, XY_Plot_1, newick_display, mothur_sub_sample, mothur_summary_single, mothur_make_biom, mothur_venn, mothur_make_shared, mothur_heatmap_sim, mothur_dist_shared, mothur_screen_seqs, mothur_get_groups, mothur_count_seqs, mothur_cluster_split, mothur_remove_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_remove_groups, mothur_cluster, taxonomy_krona_chart, mothur_count_groups, mothur_dist_seqs, mothur_chimera_vsearch, mothur_tree_shared UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 44 4.613636363636363 3646 5683 3.1333333333333333 0 +Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Local alignment, Sequence composition calculation, Sequence alignment analysis, Global alignment, Variant calling, Validation, Sequencing quality control, Phylogenetic tree generation, Antimicrobial resistance prediction, Taxonomic classification, Genome visualisation, Statistical calculation, Sequence alignment, Sequence analysis, Phylogenetic tree visualisation, Sequence contamination filtering 2020-07-25 2024-06-12 75 True False False True tb_variant_filter, bcftools_consensus, jvarkit_wgscoverageplotter, fastp, jbrowse, snippy, kraken2, EMBOSS:%20seqret84, qualimap_bamqc, fastqc, tb_profiler_profile, EMBOSS: seqret84, mosdepth, tbvcfreport, __FLATTEN__, multiqc, upload1, tp_sed_tool, samtools_stats, tp_awk_tool 25 4.64 5340 8587 2.966666666666667 0 +Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome annotation, Genome visualisation, Read mapping 2024-01-23 2024-03-13 9 True False False True upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 726 1061 3.066666666666667 0 +Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2023-02-15 19 True False False True raxml, interactive_tool_rstudio, upload1 UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 6 4.333333333333333 1211 1857 2.2666666666666666 0 +Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2022-03-16 2024-03-12 15 True False False True snippy, tb_variant_filter, tp_replace_in_line, trimmomatic, bcftools_consensus, snp_sites, tp_sed_tool, addName, tp_cat, upload1, collapse_dataset, Grep1, __MERGE_COLLECTION__, tp_easyjoin_tool, tb_profiler_profile, samtools_view, tp_grep_tool, snp_dists UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 7 4.0 1377 2211 3.183333333333333 0 +Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Statistical inference, Quantification, Functional clustering, Visualisation, Filtering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Heat map generation 2020-10-29 2024-03-14 36 True False False True metaquantome_filter, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_db, metaquantome_stat UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 357 487 2.7333333333333334 0 +Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Prediction and recognition, Visualisation 2017-06-28 2024-05-29 57 True False False True search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 1 5.0 2198 3676 2.683333333333333 0 +Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Prediction and recognition, Formatting, Visualisation, Label-free quantification, Filtering 2020-10-16 2024-03-14 90 True False False True flashlfq, Cut1, tp_replace_in_line, Remove beginning1, tp_replace_in_column, Grep1, unipept, peptide_shaker, regex1, msconvert, query_tabular, Filter1, search_gui UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 757 1325 3.8666666666666667 0 +Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Statistical inference, Quantification, Functional clustering, Visualisation, Filtering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Heat map generation 2020-10-29 2024-03-14 38 True False False True metaquantome_filter, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_db, metaquantome_stat UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 337 489 3.8666666666666667 0 +Variant Analysis Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Sequence composition calculation, Sequence alignment analysis, Generation, Sequence alignment, Variant calling, Genome indexing, Sequencing quality control, Formatting, Read mapping, Statistical calculation, Data handling 2017-02-16 2024-03-14 39 True False False True picard_MergeSamFiles, fastqc, Cut1, picard_MarkDuplicates, freebayes, vcf2tsv, bamFilter, bwa_mem, bamleftalign, vcffilter2 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 3 2.3333333333333335 6849 13178 2.05 0 +Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Local alignment, Sequence composition calculation, Sequence alignment analysis, Global alignment, Variant calling, Validation, Sequencing quality control, Phylogenetic tree generation, Antimicrobial resistance prediction, Taxonomic classification, Genome visualisation, Statistical calculation, Sequence alignment, Sequence analysis, Phylogenetic tree visualisation, Sequence contamination filtering 2020-07-25 2024-06-12 75 True False False True tb_variant_filter, bcftools_consensus, jvarkit_wgscoverageplotter, fastp, jbrowse, snippy, kraken2, EMBOSS:%20seqret84, qualimap_bamqc, fastqc, tb_profiler_profile, EMBOSS: seqret84, mosdepth, tbvcfreport, __FLATTEN__, multiqc, upload1, tp_sed_tool, samtools_stats, tp_awk_tool 25 4.64 5340 8587 2.966666666666667 0 +Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2018-02-26 2024-03-14 36 True False False True snippy, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 12 4.416666666666667 11631 19648 1.9833333333333334 0