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.
Before diving into this topic, we recommend you to have a look at:
Introduction to Genome Annotation
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|CRISPR screen analysis||plain text Toggle Dropdown||tutorial Toggle Dropdown|
|Essential genes detection with Transposon insertion sequencing||plain text Toggle Dropdown||tutorial Toggle Dropdown|
From small to large-scale genome comparison
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|Functional annotation of protein sequences||tutorial Toggle Dropdown|
|Genome annotation with Funannotate||tutorial Toggle Dropdown|
|Genome annotation with Maker||tutorial Toggle Dropdown|
|Genome annotation with Maker (short)||tutorial Toggle Dropdown|
|Genome annotation with Prokka||plain text Toggle Dropdown||tutorial Toggle Dropdown|
|Masking repeats with RepeatMasker||tutorial Toggle Dropdown|
|Refining Genome Annotations with Apollo||plain text Toggle Dropdown||tutorial Toggle Dropdown|
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 QuestionsCommon 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.
This material is maintained by:Helena Rasche Simon Gladman Anthony Bretaudeau
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:Anthony Bretaudeau Helena Rasche Maria Doyle Kenji Fujihara Twishi Gulati Delphine Lariviere Bérénice Batut Esteban Perez-Wohlfeil Anika Erxleben Björn Grüning Anna Syme Torsten Seemann Simon Gladman Alexandre Cormier Laura Leroi Erwan Corre Stéphanie Robin Erasmus+ Programme Nathan Dunn Mateo Boudet