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 RascheKenji Fujihara avatar Kenji Fujiharaorcid logoPaul Zierep avatar Paul Ziereporcid logoAnna Syme avatar Anna SymeAvans Hogeschool avatar Avans HogeschoolEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilBazante Sanders avatar Bazante SandersAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaura Leroi avatar Laura Leroiorcid logoSimon Gladman avatar Simon Gladmanorcid logoSaskia Hiltemann avatar Saskia HiltemannTwishi Gulati avatar Twishi Gulatiorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMateo Boudet avatar Mateo Boudetorcid logoBjörn Grüning avatar Björn GrüningTorsten Seemann avatar Torsten Seemannorcid logoMaria Doyle avatar Maria Doyleorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoErwan Corre avatar Erwan CorreNathan Dunn avatar Nathan Dunnorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnika Erxleben avatar Anika Erxleben

Funders

This material was funded by:

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