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
Introduction to Genome Annotation


Annotation of prokaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
Genome annotation with Prokka
Identification of AMR genes in an assembled bacterial genome
Refining Genome Annotations with Apollo (prokaryotes)
Essential genes detection with Transposon insertion sequencing


Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
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


Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
From small to large-scale genome comparison
Comparative gene analysis in unannotated genomes

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.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnthony Bretaudeau avatar 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:

Kenji Fujihara avatar Kenji FujiharaTorsten Seemann avatar Torsten Seemannorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLaura Leroi avatar Laura Leroiorcid logoSimon Gladman avatar Simon Gladmanorcid logoMaria Doyle avatar Maria Doyleorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnna Syme avatar Anna Symeorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoNathan Dunn avatar Nathan Dunnorcid logoErwan Corre avatar Erwan Correorcid logoAnthony Bretaudeau avatar Anthony BretaudeauEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoBjörn Grüning avatar Björn Grüningorcid logoPaul Zierep avatar Paul ZierepBazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSaskia Hiltemann avatar Saskia HiltemannAvans Hogeschool avatar Avans Hogeschoolorcid logoMateo Boudet avatar Mateo BoudetTwishi Gulati avatar Twishi Gulatiorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBérénice Batut avatar Bérénice Batut


This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesEuroScienceGateway avatar EuroScienceGatewayABRomics avatar ABRomics