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.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Genome Annotation
slides
Essential genes detection with Transposon insertion sequencing
plain text tutorial
From small to large-scale genome comparison
plain text tutorial
Genome annotation with Maker
tutorial
Genome annotation with Maker (short)
tutorial
Genome annotation with Prokka
plain text tutorial
Refining Genome Annotations with Apollo
plain text tutorial

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:

AvatarHelena RascheAvatarSimon GladmanAvatarAnthony Bretaudeau

For 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 BretaudeauHelena RascheDelphine LariviereBérénice BatutEsteban Perez-WohlfeilAnna SymeTorsten SeemannSimon GladmanNathan DunnMateo Boudet