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.

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
Introduction to Genome Annotation

Prokaryotes

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

Eukaryotes

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

Other

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 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.

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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.

Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoStéphanie Robin avatar Stéphanie RobinAvans Hogeschool avatar Avans Hogeschoolorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoPaul Zierep avatar Paul ZierepTwishi Gulati avatar Twishi Gulatiorcid logoAnna Syme avatar Anna SymeNathan Dunn avatar Nathan Dunnorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria Doyleorcid logoMiaomiao Zhou avatar Miaomiao ZhouAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAlexandre Cormier avatar Alexandre CormierKenji Fujihara avatar Kenji FujiharaEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilTorsten Seemann avatar Torsten Seemannorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoHelena Rasche avatar Helena RascheBazante Sanders avatar Bazante Sandersorcid logoLaura Leroi avatar Laura Leroiorcid logoBérénice Batut avatar Bérénice Batutorcid logoSimon Gladman avatar Simon Gladmanorcid logoMateo Boudet avatar Mateo Boudetorcid logoErwan Corre avatar Erwan Corre

Funders

This material was funded by:

ABRomics avatar ABRomicsGallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesEuroScienceGateway avatar EuroScienceGateway