Anthony Bretaudeau
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
- Computational chemistry / High Throughput Molecular Dynamics and Analysis π§
- Sequence analysis / SARS-CoV-2 Viral Sample Alignment and Variant Visualization π§
- Sequence analysis / Quality Control βοΈ π§
- Sequence analysis / Mapping π§
- Transcriptomics / De novo transcriptome reconstruction with RNA-Seq π§
- Transcriptomics / RNA-Seq analysis with AskOmics Interactive Tool βοΈ π§
- Transcriptomics / RNA-seq Alignment with STAR π§
- Transcriptomics / RNA Seq Counts to Viz in R π§
- Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis βοΈ
- Statistics and machine learning / Introduction to Machine Learning using R π§
- Contributing to the Galaxy Training Material / Creating content in Markdown π§
- Contributing to the Galaxy Training Material / Creating a new tutorial π§
- Contributing to the Galaxy Training Material / Including a new topic π§
- Visualisation / Genomic Data Visualisation with JBrowse π§
- Visualisation / Visualisation with Circos π§
- Genome Annotation / Dataset construction for bacterial comparative genomics π§
- Genome Annotation / Genome annotation with Braker3 βοΈ
- Genome Annotation / Genome annotation with Helixer βοΈ π§
- Genome Annotation / CRISPR screen analysis π§
- Genome Annotation / Comparative gene analysis in unannotated genomes π§
- Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc π π§
- Genome Annotation / Bacterial genome quality control π§
- Genome Annotation / Genome annotation with Maker βοΈ π§
- Genome Annotation / Identification of AMR genes in an assembled bacterial genome π§
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) βοΈ π§
- Genome Annotation / Genome annotation with Funannotate βοΈ π§
- Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) βοΈ π§
- Genome Annotation / Masking repeats with RepeatMasker βοΈ π§
- Genome Annotation / Genome annotation with Maker (short) βοΈ π§
- Genome Annotation / Creating an Official Gene Set βοΈ π§
- Genome Annotation / Functional annotation of protein sequences βοΈ
- Genome Annotation / Genome annotation with Prokka π§
- Genome Annotation / Bacterial Genome Annotation π§
- Genome Annotation / Bacterial pangenomics π§
- Introduction to Galaxy Analyses / Galaxy Basics for everyone π§
- Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) π§
- Assembly / Chloroplast genome assembly π§
- Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data π§
- Assembly / Making sense of a newly assembled genome π§
- Assembly / Genome Assembly Quality Control βοΈ π§
- Assembly / Genome assembly using PacBio data βοΈ π§
- Assembly / Unicycler Assembly π§
- Development in Galaxy / Galaxy Interactive Tools βοΈ π§
- Development in Galaxy / Creating Galaxy tools from Conda Through Deployment π§
- Development in Galaxy / Contributing to BioBlend as a developer π§
- Proteomics / Proteogenomics 1: Database Creation π§
- Using Galaxy and Managing your Data / RStudio in Galaxy π§
- Using Galaxy and Managing your Data / InterMine integration with Galaxy π§
- Teaching and Hosting Galaxy training / Course Builder π§
- Teaching and Hosting Galaxy training / Galaxy Admin Training π§
- Teaching and Hosting Galaxy training / Asynchronous training π§
- Teaching and Hosting Galaxy training / Running a workshop as instructor π§
- Evolution / Phylogenetic analysis for bacterial comparative genomics π§
- Galaxy Server administration / Galaxy Interactive Tools βοΈ
- Galaxy Server administration / Performant Uploads with TUS π§
- Galaxy Server administration / Galaxy Monitoring with Reports π§
- Galaxy Server administration / Galaxy Installation with Ansible π
- Galaxy Server administration / Automation with Jenkins π§
- Galaxy Server administration / Deploying a compute cluster in OpenStack via Terraform π§
- Galaxy Server administration / Distributed Object Storage π§
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs π§
- Galaxy Server administration / Data Libraries π§
- Galaxy Server administration / Galaxy Tool Management with Ephemeris π§
- Galaxy Server administration / Ansible π§
- Foundations of Data Science / Variant Calling Workflow π§
- Foundations of Data Science / Advanced CLI in Galaxy π§
- Foundations of Data Science / Introduction to Python π§
- Foundations of Data Science / SQL with R π§
- Foundations of Data Science / dplyr & tidyverse for data processing π§
- Foundations of Data Science / Advanced Python π§
- Foundations of Data Science / SQL with Python π§
- Foundations of Data Science / CLI basics π§
- Foundations of Data Science / Plotting in Python π§
- Foundations of Data Science / Advanced SQL π§
- Foundations of Data Science / SQL Educational Game - Murder Mystery π§
- Foundations of Data Science / Advanced R in Galaxy π§
- Foundations of Data Science / R basics in Galaxy π§
- Foundations of Data Science / Make & Snakemake π§
- Foundations of Data Science / CLI Educational Game - Bashcrawl π§
- Foundations of Data Science / Introduction to SQL π§
- Variant Analysis / M. tuberculosis Variant Analysis π§
- Variant Analysis / Calling very rare variants π§
- Variant Analysis / Microbial Variant Calling π§
- Single Cell / Single-cell quality control with scater π§
- Single Cell / Pre-processing of Single-Cell RNA Data π§
- Single Cell / Clustering 3K PBMCs with Scanpy π§
- Single Cell / Downstream Single-cell RNA analysis with RaceID π§
- Ecology / Species distribution modeling π§
Slides
- Sequence analysis / Quality Control βοΈ π§
- Sequence analysis / Mapping π§
- Transcriptomics / Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies βοΈ π§
- Visualisation / Visualisations in Galaxy π§
- Visualisation / JBrowse π§
- Visualisation / Circos π§
- Genome Annotation / Introduction to Genome Annotation βοΈ π§
- Genome Annotation / Refining Genome Annotations with Apollo βοΈ π§
- Introduction to Galaxy Analyses / Introduction to Galaxy π§
- Introduction to Galaxy Analyses / Options for using Galaxy βοΈ
- Assembly / Deeper look into Genome Assembly algorithms βοΈ
- Assembly / Genome assembly and assembly QC - Introduction short version π
- Assembly / An introduction to get started in genome assembly and annotation π π§
- Assembly / Genome assembly quality control. βοΈ π§
- Development in Galaxy / Tool Shed: sharing Galaxy tools βοΈ π§
- Development in Galaxy / Prerequisites for building software/conda packages βοΈ π§
- Development in Galaxy / Galaxy Code Architecture π§
- Development in Galaxy / Tool development and integration into Galaxy βοΈ π§
- Development in Galaxy / Tool Dependencies and Conda π§
- Galaxy Server administration / Galaxy Interactive Tools βοΈ π§
- Galaxy Server administration / Server: Other π§
- Galaxy Server administration / Storage Management π§
- Galaxy Server administration / Ansible π§
Video Recordings
- Genome Annotation / Refining Genome Annotations with Apollo π¬
- Genome Annotation / Genome annotation with Prokka π¬
- Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc π¬
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) π¬ π£
- Genome Annotation / Genome annotation with Funannotate π¬ π£
- Genome Annotation / Masking repeats with RepeatMasker π¬ π£
- Genome Annotation / Genome annotation with Prokka π¬ π£
- Galaxy Server administration / Galaxy Interactive Tools π¬ π£
Events
- Galaxy Training Academy 2025 π§βπ«
- Galaxy Training Academy 2024 π§βπ«
GitHub Activity
github Issues Reported
67 Merged Pull Requests
See all of the github Pull Requests and github Commits by Anthony Bretaudeau.
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Update Jbrowse parameter
variant-analysisassemblygenome-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-toolsgenome-annotation -
Annotation learning paths
template-and-toolsgenome-annotation
Reviewed 64 PRs
We love our community reviewing each other's work!
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Added training on Braker3
genome-annotation -
Draft tutorials for bacterial comparative genomics learning pathway
template-and-toolsgenome-annotationevolution -
Add jupyterlab stuff & other small updates
dev -
Add Helixer training
genome-annotation -
Update slides.html
genome-annotation
News

New Tutorial: Genome Annotation with Apollo
4 June 2021
After two years, the Galaxy Genome Annotation team has finally finished their much awaited tutorial on doing Genome Annotation in Galaxy! Genome annotation is a time consuming and largely manual process as it requires the synthesis of a significant amount of varied information to make inferences, a process tha cannot be accomplished without an interactive editor. To support this, Apollo was deployed on UseGalaxy.eu. Over the past two years the GGA project has pushed forward apollo and tooling around it, and it finally culminates in this look at how to annotated your genomes in Apollo.
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