diff --git a/content/assets/media/gnb.png b/content/assets/media/gnb.png new file mode 100644 index 0000000000..ab15d14bc0 Binary files /dev/null and b/content/assets/media/gnb.png differ diff --git a/content/news/2023-10-30-gga-update/index.md b/content/news/2023-10-30-gga-update/index.md new file mode 100644 index 0000000000..8f308cc127 --- /dev/null +++ b/content/news/2023-10-30-gga-update/index.md @@ -0,0 +1,186 @@ +--- +title: "An update on Galaxy Genome Annotation" +tease: "Galaxy as a platform for the annotation of genomes" +authors: "Anthony Bretaudeau, Romane Libouban, Helena Rasche, Björn Gruening, and all other GGA contributors" +date: "2023-10-30" +hide_tease: false +tags: [esg-wp5, esg] +subsites: [all, all-eu, esg] +--- + +## Galaxy Genome Annotation + +As presented at GCC2023 and EGD2023, a lot of new exciting developments have been made in Galaxy for the annotation of genomes! + +This has been done in the frame of the GGA community of practice that you are really welcome to join if you have interest in genome annotation within Galaxy (as a user, developer, trainer, ...). + +## New tools! + +We've worked hard to integrate into Galaxy many state-of-the-art genome annotation tools! Here's the complete, categorized, list: + +### Repeated elements detection + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| RepeatModeler | 2.0.4 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1) | +| RepeatMasker | 4.1.5 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0) | +| Red | 2018.09.10 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1) | + +### Gene detection for prokaryotes + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| Prokka | 1.14.6 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.6+galaxy1) | +| Bakta | 1.8.2 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0) | + +### Gene detection for eukaryotes + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| BRAKER3 | 3.0.3 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.3+galaxy1) | +| BRAKER2 | 2.1.6 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/genouest/braker/braker/2.1.6+galaxy0) | +| Helixer | 0.3.2 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.2) | +| Funannotate | 1.8.15 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1) | +| MAKER | 2.31.11 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11+galaxy2) | +| TSEBRA | 1.1.1 | Available soon | + +### Functional annotation + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| Antismash | 6.1.1 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1) | +| InterProScan | 5.59-91 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3) | +| EggNOG-Mapper | 2.1.8 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy4) | +| DeepSig | 1.2.5 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/deepsig/deepsig/1.2.5+galaxy0) | + +### Evaluation methods + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| Genome annotation statistics | 0.8.4 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4) | +| BUSCO | 5.4.6 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0) | + +### Annotation comparison + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| AEGeAN | 0.16.0 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0) | +| Funannotate compare | 1.8.15 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1) | + +### General alignment tools + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| BLAST | 2.14.1 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy0) | +| Exonerate | 2.4.0 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0+galaxy2) | +| Diamond | 2.0.15 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0) | +| Miniprot | 0.12 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/miniprot/miniprot/0.12+galaxy0) | + +### Long non-coding RNA prediction + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| FEELnc | 0.2.1 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1+galaxy0) | + +### Visualisation + +| Tool | Version | UseGalaxy.eu | +|---|---|---|---|---| +| JBrowse | 1.16.11 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1) | +| Circos | 0.69.8 | [link](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9) | +| GeneNoteBook | 0.4.8 | [link](https://usegalaxy.fr/root?tool_id=toolshed.g2.bx.psu.edu/repos/gga/genenotebook_genenotebook_build/genenotebook_build/0.4.8+galaxy0) | + +## New workflows! + +Over the last years we have collected a lot of different workflows for different use-cases. All the GTN tutorials below, for example, are also +available as workflows. However, they might be hard to find and as a consequence people can be tempted to redo them. To fix that we +have started to push our workflows to the Intergalactic Workflow Commission, adding workflow tests and pushing them to workflowhub.eu and Dockstore for +broader dissemination. + +You can see the first IWC workflow from the GGA community at [workflowhub](https://workflowhub.eu/workflows/575) or on [GitHub as part of the IWC organisation](https://github.com/iwc-workflows/repeatmasking). + +Next up is the [functional annotation](https://github.com/galaxyproject/iwc/pull/228) workflow and our GTN workflows - see below. + +## New visualisations! + +Galaxy is much more than just a workflow system and one area that we are trying to improve is Visualisation! + +Check out our tutorials about this: + +![JBrowse](/assets/media/jbrowse.png) + + + +![Circos](/assets/media/circos.png) + + + +We also added support for GeneNoteBook: a nice way to present functional annotation data into an easy-to-navigate website: + +![GeneNoteBook](/assets/media/gnb.png) + + +## New and updated training material! + +We have updated and added new training material for everyone that wants to learn Genome Annotation. If you don't know where to start check out our +recommended learning path and learn from "Introduction to Genome Annotation" to "Refining Genome Annotations with Apollo" everything that you need to know about Genome Annotation: + + + +Alternatively, you can jump right into you favorite topic: + + + + + + + + + + + + + + + + + +## Manual curation and collaborative annotation made easy + +[Apollo](https://genomearchitect.readthedocs.io/en/latest/) is a web service for Collaborative Annotation - a “Google Docs of Genome Annotation” +if you like to think in Google Terms. It allows for real-time, collaborative genome annotation, editing, and review of your favorite genome. +Genome Annotation requires manual curation and review many hands are needed - +Biology is a team sport! And Apollo is a wonderful tool to support your team. + +![Galaxy Apollo integration](/assets/media/collaborative_editing.png) + +To make your life easy we worked closely with the Apollo team and bridged Galaxy with Apollo. +You can do automatic annotation with Galaxy, using its powerful workflow system, and afterwards send +the data to Apollo for manual curation and collaborative editing! A typical Galaxy-Apollo use-case might look like that: + + 1. Fetch Data + 2. Analyse in Galaxy + 3. Send to Apollo + 4. Collaboratively Annotate + → repeat + +![Galaxy Apollo integration](/assets/media/galaxy_apollo.png) + + +## The Earth BioGenome Project + +Building on the [Assembly workflows](https://galaxyproject.org/projects/vgp/) that have been developed as part of the [VGP](https://vertebrategenomesproject.org/)/[BGE](https://biodiversitygenomics.eu/)/[ERGA](https://www.erga-biodiversity.eu/) (→ in short [EBP](https://www.earthbiogenome.org/)) we are planning to deliver high-quality workflows and interactive tools for your genome annotation efforts. Ideally, running assembly and annnotation workflows after each other 😊 + +## What's next? + +Any tool or workflow missing in our catalog? Please tell us and we will do our best to make it available! + +We already have these items on our TODO list, stay tuned: + +- JBrowse2 +- GALBA +- OMark +- BUSCO update +- InterProScan update + +Join us on our [chat channel](https://matrix.to/#/#galaxy-genome-annotation_Lobby:gitter.im) to keep in touch!