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 (slides) and tutorial (tutorial) buttons below.


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



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
plain text


Annotation of prokaryotic genomes.

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


    Annotation of eukaryotic genomes.

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

    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.


    This material is maintained by:

    orcid logoAvatarHelena Rascheorcid logoAvatarSimon Gladmanorcid logoAvatarAnthony 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:

    orcid logoAvatarAnthony Bretaudeauorcid logoAvatarHelena RascheAvatarEsteban Perez-Wohlfeilorcid logoAvatarAnika Erxlebenorcid logoAvatarBjörn GrüningAvatarAnna SymeAvatarTorsten Seemannorcid logoAvatarSimon GladmanAvatarNathan Dunnorcid logoAvatarMateo BoudetAvatarErasmus+ Programmeorcid logoAvatarAlexandre Cormierorcid logoAvatarLaura Leroiorcid logoAvatarErwan Correorcid logoAvatarStéphanie Robinorcid logoAvatarJonathan KreplakAvatarAnton NekrutenkoAvatarDelphine Lariviereorcid logoAvatarBérénice BatutAvatarMaria DoyleAvatarKenji FujiharaAvatarTwishi Gulati