Anthony Bretaudeau
Favourite Topics
Favourite Formats
Contributions
The following list includes only slides and tutorials where the individual 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.
GitHub Activity
Tutorials
- Development in Galaxy / Galaxy Interactive Tools
- Genome Annotation / Genome annotation with Funannotate
- Genome Annotation / Refining Genome Annotations with Apollo
- Genome Annotation / Masking repeats with RepeatMasker
- Genome Annotation / Genome annotation with Maker (short)
- Genome Annotation / Genome annotation with Maker
- Assembly / Genome assembly using PacBio data
- Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
- Transcriptomics / RNA-Seq analysis with AskOmics Interactive Tool
- Sequence analysis / Quality Control
- Galaxy Server administration / Galaxy Interactive Tools
Slides
- Genome Annotation / Introduction to Genome Annotation
- Development in Galaxy / Tool development and integration into Galaxy
- Development in Galaxy / Prerequisites for building software/conda packages
- Development in Galaxy / Tool Shed: sharing Galaxy tools
- Introduction to Galaxy Analyses / Options for using Galaxy
- Genome Annotation / Refining Genome Annotations with Apollo
- Assembly / An introduction to get started in genome assembly and annotation 📝
- Assembly / Deeper look into Genome Assembly algorithms
- Transcriptomics / Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies
- Sequence analysis / Quality Control
- Galaxy Server administration / Galaxy Interactive Tools
News
We have just finished a new collection of training material for genome assembly and annotation! You now have access to slides and tutorials, focused on the complete analysis of the genome of a fungus species (Mucor mucedo).
Full StoryAs part of our work under the Gallantries Grant we are establishing a new topic within the GTN specifically focused on Data Science skills. This topic will include tutorials covering things such as:
Full StoryAfter 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.
Full Story