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.
Before diving into this topic, we recommend you to have a look at:
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Introduction to Genome Annotation
Essential genes detection with Transposon insertion sequencing
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Genome annotation with Maker
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Genome annotation with Prokka
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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.
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, Delphine Lariviere, Bérénice Batut, Anna Syme, Torsten Seemann, Simon Gladman