Genome Annotation
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Requirements
Before diving into this topic, we recommend you to have a look at:
Material
Introduction
Start here if you are new to genome annotation in Galaxy.Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows | Galaxy servers |
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Introduction to Genome Annotation
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plain text Toggle Dropdown |
Prokaryotes
Annotation of prokaryotic genomes.Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows | Galaxy servers |
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Genome annotation with Prokka | plain text Toggle Dropdown | tutorial Toggle Dropdown |
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Refining Genome Annotations with Apollo (prokaryotes) | plain text Toggle Dropdown | tutorial Toggle Dropdown |
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Essential genes detection with Transposon insertion sequencing | plain text Toggle Dropdown | tutorial Toggle Dropdown | instances |
Eukaryotes
Annotation of eukaryotic genomes.Other
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows | Galaxy servers |
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From small to large-scale genome comparison
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plain text Toggle Dropdown | tutorial Toggle Dropdown | instances | |||
Comparative gene analysis in unannotated genomes | tutorial Toggle Dropdown | instances |
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/genome-annotation-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked Questions
Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.Maintainers
This material is maintained by:
Helena Rasche Simon Gladman Anthony BretaudeauFor any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Anthony Bretaudeau Helena Rasche Esteban Perez-Wohlfeil Anika Erxleben Björn Grüning Anna Syme Torsten Seemann Simon Gladman Nathan Dunn Mateo Boudet Erasmus+ Programme Alexandre Cormier Laura Leroi Erwan Corre Stéphanie Robin Jonathan Kreplak Anton Nekrutenko Delphine Lariviere Bérénice Batut Maria Doyle Kenji Fujihara Twishi Gulati