Anthony Bretaudeau

Affiliations

Former Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Genome Annotation
• Topic: GMOD
• Learning Pathway: Genome annotation for eukaryotes
• Learning Pathway: Genome annotation for prokaryotes
• Learning Pathway: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration

Tutorials

• Genome Annotation / Comparative gene analysis in unannotated genomes 🧐
• Genome Annotation / Bacterial Genome Annotation 🧐
• Genome Annotation / Genome annotation with Braker3 ✍️ 🧐
• Genome Annotation / CRISPR screen analysis 🧐
• Genome Annotation / Bacterial pangenomics 🧐
• Genome Annotation / Genome annotation with Prokka 🧐
• Genome Annotation / Creating an Official Gene Set ✍️ 🧐
• Genome Annotation / Masking repeats with RepeatMasker ✍️ 🧐
• Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) ✍️ 🧐
• Genome Annotation / Genome annotation with Helixer ✍️ 🧐
• Genome Annotation / Genome annotation with Funannotate ✍️ 🧐
• Genome Annotation / Dataset construction for bacterial comparative genomics 🧐
• Genome Annotation / Bacterial genome quality control 🧐
• Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc 📝 🧐
• Genome Annotation / Genome annotation with Maker (short) ✍️ 🧐
• Genome Annotation / Genome annotation with Maker ✍️ 🧐
• Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) ✍️ 🧐
• Genome Annotation / Identification of AMR genes in an assembled bacterial genome 🧐
• Genome Annotation / Functional annotation of protein sequences ✍️
• Evolution / Phylogenetic analysis for bacterial comparative genomics 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Teaching and Hosting Galaxy training / Running a workshop as an instructor 🧐
• Teaching and Hosting Galaxy training / Course Builder 🧐
• Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
• Teaching and Hosting Galaxy training / Asynchronous training 🧐
• Single Cell / Downstream Single-cell RNA analysis with RaceID 🧐
• Single Cell / Single-cell quality control with scater 🧐
• Single Cell / Clustering 3K PBMCs with Scanpy 🧐
• Single Cell / Pre-processing of Single-Cell RNA Data 🧐
• Variant Analysis / Microbial Variant Calling 🧐
• Variant Analysis / M. tuberculosis Variant Analysis 🧐
• Variant Analysis / Calling very rare variants 🧐
• Sequence analysis / SARS-CoV-2 Viral Sample Alignment and Variant Visualization 🧐
• Sequence analysis / Quality Control ✍️ 🧐
• Sequence analysis / Mapping 🧐
• Visualisation / Genomic Data Visualisation with JBrowse 🧐
• Visualisation / Visualisation with Circos 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Galaxy Interactive Tools ✍️
• Galaxy Server administration / Performant Uploads with TUS 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports 🧐
• Galaxy Server administration / Deploying a compute cluster in OpenStack via Terraform 🧐
• Galaxy Server administration / Automation with Jenkins 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 📝
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
• Galaxy Server administration / Data Libraries 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Proteomics / Proteogenomics 1: Database Creation 🧐
• Using Galaxy and Managing your Data / InterMine integration with Galaxy 🧐
• Using Galaxy and Managing your Data / RStudio in Galaxy 🧐
• Computational chemistry / High Throughput Molecular Dynamics and Analysis 🧐
• Ecology / Species distribution modeling 🧐
• Foundations of Data Science / R basics in Galaxy 🧐
• Foundations of Data Science / Make & Snakemake 🧐
• Foundations of Data Science / SQL Educational Game - Murder Mystery 🧐
• Foundations of Data Science / Variant Calling Workflow 🧐
• Foundations of Data Science / Advanced CLI in Galaxy 🧐
• Foundations of Data Science / Introduction to Python 🧐
• Foundations of Data Science / Introduction to SQL 🧐
• Foundations of Data Science / dplyr & tidyverse for data processing 🧐
• Foundations of Data Science / Advanced SQL 🧐
• Foundations of Data Science / CLI Educational Game - Bashcrawl 🧐
• Foundations of Data Science / SQL with Python 🧐
• Foundations of Data Science / Advanced Python 🧐
• Foundations of Data Science / Plotting in Python 🧐
• Foundations of Data Science / CLI basics 🧐
• Foundations of Data Science / SQL with R 🧐
• Foundations of Data Science / Advanced R in Galaxy 🧐
• Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
• Transcriptomics / RNA-Seq analysis with AskOmics Interactive Tool ✍️ 🧐
• Transcriptomics / RNA Seq Counts to Viz in R 🧐
• Transcriptomics / RNA-seq Alignment with STAR 🧐
• Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis ✍️
• Contributing to the Galaxy Training Material / Including a new topic 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Statistics and machine learning / Introduction to Machine Learning using R 🧐
• Assembly / Genome assembly using PacBio data ✍️ 🧐
• Assembly / Genome Assembly Quality Control ✍️ 🧐
• Assembly / Unicycler Assembly 🧐
• Assembly / Making sense of a newly assembled genome 🧐
• Assembly / Chloroplast genome assembly 🧐
• Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) 🧐
• Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data 🧐
• Development in Galaxy / Galaxy Interactive Tools ✍️ 🧐
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 🧐
• Development in Galaxy / Contributing to BioBlend as a developer 🧐
• Sequence analysis / Qualitätskontrolle ✍️
• Sequence analysis / Control de calidad ✍️
• Sequence analysis / Controllo qualità ✍️

Slides

• Genome Annotation / Introduction to Genome Annotation ✍️ 🧐
• Genome Annotation / Refining Genome Annotations with Apollo ✍️ 🧐
• Introduction to Galaxy Analyses / Introduction to Galaxy 🧐
• Introduction to Galaxy Analyses / Options for using Galaxy ✍️
• Sequence analysis / Quality Control ✍️ 🧐
• Sequence analysis / Mapping 🧐
• Visualisation / Visualisations in Galaxy 🧐
• Visualisation / JBrowse 🧐
• Visualisation / Circos 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Galaxy Interactive Tools ✍️ 🧐
• Galaxy Server administration / Storage Management 🧐
• Galaxy Server administration / Server: Other 🧐
• Transcriptomics / Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies ✍️ 🧐
• Assembly / Genome assembly quality control. ✍️ 🧐
• Assembly / Deeper look into Genome Assembly algorithms ✍️
• Assembly / Genome assembly and assembly QC - Introduction short version 📝 🧐
• Assembly / An introduction to get started in genome assembly and annotation 📝 🧐
• Development in Galaxy / Prerequisites for building software/conda packages ✍️ 🧐
• Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
• Development in Galaxy / Tool Shed: sharing Galaxy tools ✍️ 🧐
• Development in Galaxy / Tool Dependencies and Conda 🧐

Video Recordings

• Genome Annotation / Genome annotation with Prokka 💬
• Genome Annotation / Refining Genome Annotations with Apollo 💬
• Genome Annotation / Genome annotation with Prokka 💬 🗣
• Genome Annotation / Masking repeats with RepeatMasker 💬 🗣
• Genome Annotation / Genome annotation with Funannotate 💬 🗣
• Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc 💬
• Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 💬 🗣
• Galaxy Server administration / Galaxy Interactive Tools 💬 🗣

Events

• Galaxy Training Academy 2025 🧑‍🏫
• Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability 🎪 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

68 Merged Pull Requests

See all of the github Pull Requests and github Commits by Anthony Bretaudeau.

• Fix typo on GTA2025 news
  news
• Update Jbrowse parameter
  variant-analysis
  assembly
  genome-annotation
• Fix input data for apollo tutorial (fixes #5792)
  genome-annotation
• Update abretaud infos
  template-and-tools
• Add eurosciencegateway affiliation to some GGA stuff
  template-and-tools
  genome-annotation

Reviewed 72 PRs

We love our community reviewing each other's work!

• Galaxy Formation Avancée 2026
  template-and-tools
• add training comparison annotation
  genome-annotation
• Update training assembly
  template-and-tools
  assembly
• Update tuto assembly pacbio hifi
  assembly
• Updated slides on short assembly/QC training to include srobin feedback
  assembly

News

External Links

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