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.
Full StoryAnthony Bretaudeau
Affiliations
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
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.
- Genome Annotation
- GMOD
- Genome annotation for eukaryotes
- Genome annotation for prokaryotes
- Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration
Tutorials
- Galaxy Server administration / Galaxy Installation with Ansible 📝
- Galaxy Server administration / Galaxy Interactive Tools ✍️
- Transcriptomics / RNA-Seq analysis with AskOmics Interactive Tool
- Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
- Genome Annotation / Genome annotation with Maker
- Genome Annotation / Genome annotation with Maker (short)
- Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc 📝
- Genome Annotation / Creating an Official Gene Set ✍️
- Genome Annotation / Genome annotation with Funannotate ✍️
- Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) ✍️
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) ✍️
- Genome Annotation / Functional annotation of protein sequences ✍️
- Genome Annotation / Genome annotation with Helixer ✍️
- Genome Annotation / Masking repeats with RepeatMasker ✍️
- Sequence analysis / Quality Control
- Development in Galaxy / Galaxy Interactive Tools
- Assembly / Genome assembly using PacBio data
- Assembly / Genome Assembly Quality Control
Slides
- Introduction to Galaxy Analyses / Options for using Galaxy
- Galaxy Server administration / Galaxy Interactive Tools
- Transcriptomics / Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies
- Genome Annotation / Introduction to Genome Annotation
- Genome Annotation / Refining Genome Annotations with Apollo
- Sequence analysis / Quality Control
- Development in Galaxy / Prerequisites for building software/conda packages
- Development in Galaxy / Tool Shed: sharing Galaxy tools
- Development in Galaxy / Tool development and integration into Galaxy
- Assembly / Deeper look into Genome Assembly algorithms
- Assembly / An introduction to get started in genome assembly and annotation 📝
- Assembly / Genome assembly quality control.
Video Recordings
- Genome Annotation / Genome annotation with Prokka 💬
- Genome Annotation / Refining Genome Annotations with Apollo 💬
- Galaxy Server administration / Galaxy Interactive Tools 💬 🗣
- Genome Annotation / Genome annotation with Funannotate 💬 🗣
- Genome Annotation / Genome annotation with Prokka 💬 🗣
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 💬 🗣
- Genome Annotation / Masking repeats with RepeatMasker 💬 🗣
Events
News
As 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 StoryWe 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 StoryAuthor(s) | Helena Rasche Anthony Bretaudeau |
Infrastructure | Helena Rasche |
Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.
Full StoryExternal Links
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