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
Introduction to Genome Annotation

Prokaryotes

Annotation of prokaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
gmod illumina bacteria microgalaxy jbrowse1
Genome annotation with Prokka
gmod prokaryote microgalaxy jbrowse1
Identification of AMR genes in an assembled bacterial genome
gmod illumina amr one-health jbrowse1 microgalaxy
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 apollo2
Essential genes detection with Transposon insertion sequencing
bacteria tnseq essential genes microgalaxy

Eukaryotes

Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Masking repeats with RepeatMasker
eukaryote
Genome annotation with Funannotate
gmod eukaryote jbrowse1
Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Genome annotation with Maker
gmod eukaryote jbrowse1 maker
Functional annotation of protein sequences
eukaryote
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2
Long non-coding RNAs (lncRNAs) annotation with FEELnc
eukaryote
CRISPR screen analysis
genome editing CRISPR essential genes cell line

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
From small to large-scale genome comparison
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy

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 logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon GladmanEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoDelphine Lariviere avatar Delphine LariviereTorsten Seemann avatar Torsten Seemannorcid logoBjörn Grüning avatar Björn Grüningorcid logoMaria Doyle avatar Maria DoyleBazante Sanders avatar Bazante Sandersorcid logoMiaomiao Zhou avatar Miaomiao ZhouAvans Hogeschool avatar Avans Hogeschoolorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBérénice Batut avatar Bérénice Batutorcid logoLaura Leroi avatar Laura Leroiorcid logoMateo Boudet avatar Mateo BoudetTwishi Gulati avatar Twishi Gulatiorcid logoStéphanie Robin avatar Stéphanie RobinNathan Dunn avatar Nathan DunnKenji Fujihara avatar Kenji Fujiharaorcid logoAnthony Bretaudeau avatar Anthony BretaudeauAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoPaul Zierep avatar Paul Ziereporcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoErwan Corre avatar Erwan Corre

Funders

This material was funded by:

EuroScienceGateway avatar EuroScienceGatewayGallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesABRomics avatar ABRomics