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

Introduction

Start here if you are new to genome annotation in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
Introduction to Genome Annotation

Prokaryotes

Annotation of prokaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
Genome annotation with Prokka
    • Refining Genome Annotations with Apollo (prokaryotes)
    • Essential genes detection with Transposon insertion sequencing

    Eukaryotes

    Annotation of eukaryotic genomes.

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Masking repeats with RepeatMasker
    • Genome annotation with Funannotate
    • Genome annotation with Maker (short)
    Genome annotation with Maker
    Functional annotation of protein sequences
    Refining Genome Annotations with Apollo (eukaryotes)
    Long non-coding RNAs (lncRNAs) annotation with FEELnc
    CRISPR screen analysis

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