# Genome Annotation tooling in Galaxy: contributions of the EuroScienceGateway project

Romane Libouban, Anthony Bretaudieu

► To cite this version:

Romane Libouban, Anthony Bretaudieu. Genome Annotation tooling in Galaxy: contributions of the EuroScienceGateway project. JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-1, 2025. hal-05144157

HAL Id: hal-05144157

https://hal.science/hal-05144157v1

Submitted on 4 Jul 2025

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Distributed under a Creative Commons Attribution 4.0 International License
# Genome Annotation tooling in Galaxy: contributions of the EuroScienceGateway project

Romane LIBOUBAN¹ and Anthony BRETAUDEAU¹

¹ GenOuest, University of Rennes, INRIA, CNRS, IRISA, Rennes, France

## EuroScienceGateway Project Context

Facilitating access to computing and storage infrastructures across Europe in line with the needs of researchers in multiple scientific fields (Biodiversity, Astronomy, Climate and Material Science).

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The **GenOuest** platform, in close collaboration with the **Institut Français de Bioinformatique (IFB)**, is developing the national **UseGalaxy.fr** server by implementing technologies that enable **interoperability** between the infrastructures available throughout **Europe**. An ESG goal is to enhance maturity of **6 national Galaxy servers**, including **UseGalaxy.fr** (TRL-9).

galaxyproject.org/projects/esg

## Galaxy: an accessible web portal for FAIR data analysis

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+3K active users

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useGalaxy.fr

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+5 M jobs

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Tools List

Tool Forms/Result Viewer

History

Common set of tools and workflows, connection to Pulsar endpoints, shared reference data and Apptainer images (CVMFS), federated login, ...

## Genome Annotation Workflows

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Tools List

Workflow editor

Customize tool settings

Used by large scale genome sequencing project Earth BioGenome Project (EBP) : VGP, ERGA, ATLASea, ..

Need for standar genome annotation procedures

* Adding new Galaxy tools

* FAIR Workflows

* Online training materials

(training.galaxyproject.org/training-material)

Several workflows have been designed and made available on UseGalaxy.fr to facilitate genome annotation:

* "Annotate a genome with Braker3"

* "Annotate a genome with Helixer"

These workflows include **comprehensive steps ranging from annotation to evaluation** of results with tools such as BUSCO and OMArk, as well as interactive **visualization steps** with JBrowse.

### 1. Create a workflow or export it

Galaxy has a ** workflow editor** that allows you to create and edit workflows, making it easy to add tools, customize settings, and adapt them to specific user needs. To ensure the ** reproducibility ** of analyses, Galaxy allows users to ** import ** and ** share** workflows with others, including via the WorkflowHub platform. (https:// workflowhub.eu/).

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### 3. Visualize and analyze results

Visualize your results in a graphic and user-friendly environment. Represented here are a genome annotated with Braker3 in JBrowse or an evaluation of the annotation quality by BUSCO.

### 2. Launch your workflows

Fill in the settings and press run. You can track the progress of your analyses and restart them if they fail.

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Project 2023-2025

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Funded by the European Union

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee grant number 10038963.