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 () and tutorial () buttons below.

Requirements

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

Material

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Genome Annotation
CRISPR screen analysis
    • Essential genes detection with Transposon insertion sequencing
    From small to large-scale genome comparison
    Functional annotation of protein sequences
    Genome annotation with Funannotate
    • Genome annotation with Maker
    Genome annotation with Maker (short)
    Genome annotation with Prokka
    • Masking repeats with RepeatMasker
    • Refining Genome Annotations with Apollo

    • 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:

    orcid logoAvatarHelena Rasche AvatarSimon Gladman orcid logoAvatarAnthony 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:

    orcid logoAvatarAnthony Bretaudeau orcid logoAvatarHelena Rasche AvatarMaria Doyle AvatarKenji Fujihara AvatarTwishi Gulati AvatarDelphine Lariviere orcid logoAvatarBérénice Batut AvatarEsteban Perez-Wohlfeil orcid logoAvatarAnika Erxleben orcid logoAvatarBjörn Grüning AvatarAnna Syme AvatarTorsten Seemann AvatarSimon Gladman orcid logoAvatarAlexandre Cormier orcid logoAvatarLaura Leroi orcid logoAvatarErwan Corre orcid logoAvatarStéphanie Robin AvatarErasmus+ Programme AvatarNathan Dunn orcid logoAvatarMateo Boudet