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
Essential genes detection with Transposon insertion sequencing
bacteria tnseq essential genes microgalaxy
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

Eukaryotes

Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
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
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

Other

Assorted Tutorials

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

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:

orcid logoTeresa Müller avatar Teresa Müllerorcid logoDeepti Varshney avatar Deepti VarshneyEkaterina Polkh avatar Ekaterina PolkhWilliam Durand avatar William DurandJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoNiklas Mayle avatar Niklas MayleHélène Chiapello avatar Hélène ChiapelloEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoSaskia Hiltemann avatar Saskia HiltemannGildas Le Corguillé avatar Gildas Le CorguilléNathan Dunn avatar Nathan DunnKenji Fujihara avatar Kenji FujiharaGuillaume Gautreau avatar Guillaume GautreauNiall Beard avatar Niall Beardorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnna Syme avatar Anna Symeorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBérénice Batut avatar Bérénice Batutorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoErwan Corre avatar Erwan CorreTwishi Gulati avatar Twishi GulatiBazante Sanders avatar Bazante SandersSimon Bray avatar Simon Brayorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoHelena Rasche avatar Helena Rascheorcid logoMateo Boudet avatar Mateo Boudetorcid logoSaim Momin avatar Saim MominValentin Loux avatar Valentin Louxorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAlexandre Cormier avatar Alexandre CormierTorsten Seemann avatar Torsten Seemannorcid logoAnika Erxleben avatar Anika ErxlebenAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaura Leroi avatar Laura Leroiorcid logoBjörn Grüning avatar Björn Grüningorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPaul Zierep avatar Paul Ziereporcid logoMaria Doyle avatar Maria Doyleorcid logoSimon Gladman avatar Simon Gladman

Funding

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

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ABRomics
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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.
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Australian BioCommons
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The University of Melbourne
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Melbourne Bioinformatics
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ELIXIR Europe
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Avans
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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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IFB