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GGA in 2023 news #2235

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77 changes: 77 additions & 0 deletions content/news/2023-10-26-gga-update/index.md
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---
title: "An update on Galaxy Genome Annotation"
tease: "Galaxy as a platform for the annotation of genomes"
authors: "Anthony Bretaudeau, Romane Libouban"
date: "2023-10-26"
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 tools:

| Tool | Version | UseGalaxy.eu | UseGalaxy.org | UseGalaxy.org.au |
|---|---|---|---|---|
| RepeatModeler | | | | |
| RepeatMasker | | | | |
| Red | | | | |
| Prokka | | | | |
| Bakta | | | | |
| Helixer | | | | |
| BRAKER2 | | | | |
| BRAKER3 | | | | |
| TSEBRA | | | | |
| Funannotate | | | | |
| MAKER | | | | |
| Antismash | | | | |
| InterProScan | | | | |
| EggNOG-Mapper | | | | |
| Genome annotation statistics | | | | |
| BUSCO | | | | |
| AEGeAN | | | | |
| BLAST | | | | |
| Exonerate | | | | |
| Diamond | | | | |
| Miniprot | | | | |
| FEELnc | | | | |
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## New workflows!
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We just list all workflows here I think, not just the new ones.


- IWC repeat masking
- functional annotation https://github.com/galaxyproject/iwc/pull/228
- GTN workflows: funannotate, maker, prokka

## New visualisations!

- the existing ones: jbrowse/circos
- GNB
- install gxit on .eu (if not done?)
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Where is this tool?

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https://toolshed.g2.bx.psu.edu/repository/view_repository?id=ef69fe5507b8d8c7&changeset_revision=bd94e502872a
and
https://gitlab.com/ifb-elixirfr/usegalaxy-fr/galaxy/-/blob/release_23.0_ifb/tools/interactive/interactivetool_genenotebook.xml

Do you have time for a quick install on .eu (I can test it) or we'll see later?

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usegalaxy-eu/usegalaxy-eu-tools#638


## New training material!

- Gallantries hall of fame / learning path etc
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## Manual curation made easy

- Apollo infra, available on usegalaxy.eu/apollo
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Take content from the older blog post?


## EBP

Building on the VGP assembly workflows, doing the same for annotation
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## What's next?

Any tool or workflow missing in our catalog? Please tell us and we will do our best to make it available.

- jbrowse2
- GALBA, OMark, BUSCO/InterProScan updates

BEAURIS link?
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