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.

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Requirements

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

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

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 biodiversity 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
Comparison of two annotation tools - Helixer and Braker3
eukaryota Braker3 Helixer jbrowse1 biodiversity
Genome annotation with Braker3
eukaryota Braker3 jbrowse1 biodiversity
Genome annotation with Helixer
eukaryota helixer jbrowse1 biodiversity
Masking repeats with RepeatMasker
eukaryote biodiversity
Genome annotation with Funannotate
gmod eukaryote jbrowse1 biodiversity
Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Genome annotation with Maker
gmod eukaryote jbrowse1 maker
Functional annotation of protein sequences
eukaryote biodiversity
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity
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
plants prokaryote
Pangenome analysis with Roary
pangenome prokaryote phylogeny
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy biodiversity

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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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

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Contributors

This material was contributed to by:

Niall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine LariviereEkaterina Polkh avatar Ekaterina Polkhorcid logoNiklas Mayle avatar Niklas MayleSimon Bray avatar Simon BrayTorsten Seemann avatar Torsten Seemannorcid logoSaskia Hiltemann avatar Saskia HiltemannNathan Dunn avatar Nathan Dunnorcid logoBérénice Batut avatar Bérénice Batutorcid logoPaul Zierep avatar Paul ZierepGuillaume Gautreau avatar Guillaume Gautreauorcid logoMaria Doyle avatar Maria Doyleorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAlexandre Cormier avatar Alexandre CormierEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoMateo Boudet avatar Mateo Boudetorcid logoHelena Rasche avatar Helena RascheHélène Chiapello avatar Hélène ChiapelloValentin Loux avatar Valentin Louxorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANWilliam Durand avatar William DurandKenji Fujihara avatar Kenji Fujiharaorcid logoLaura Leroi avatar Laura Leroiorcid logoBjörn Grüning avatar Björn Grüningorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSaim Momin avatar Saim MominJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoErwan Corre avatar Erwan Correorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoSimon Gladman avatar Simon GladmanBazante Sanders avatar Bazante SandersGildas Le Corguillé avatar Gildas Le Corguilléorcid logoJonathan Kreplak avatar Jonathan KreplakTwishi Gulati avatar Twishi Gulatiorcid logoFelicitas Kindel avatar Felicitas Kindel

Funding

These individuals or organisations provided funding support for the development of this resource

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ABRomics
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IFB
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The University of Melbourne
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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ELIXIR Europe
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Avans
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Melbourne Bioinformatics
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Australian BioCommons
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.