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:

Nathan Dunn avatar Nathan Dunnorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoLaura Leroi avatar Laura Leroiorcid logoNiklas Mayle avatar Niklas MayleValentin Loux avatar Valentin LouxKenji Fujihara avatar Kenji Fujiharaorcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre CormierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPaul Zierep avatar Paul Ziereporcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoHelena Rasche avatar Helena RascheJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon BrayHélène Chiapello avatar Hélène Chiapelloorcid logoMaria Doyle avatar Maria DoyleGuillaume Gautreau avatar Guillaume GautreauTwishi Gulati avatar Twishi Gulatiorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoErwan Corre avatar Erwan CorreTorsten Seemann avatar Torsten Seemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMiaomiao Zhou avatar Miaomiao ZhouBazante Sanders avatar Bazante SandersEkaterina Polkh avatar Ekaterina PolkhGildas Le Corguillé avatar Gildas Le CorguilléWilliam Durand avatar William Durandorcid logoSaim Momin avatar Saim Mominorcid logoSaskia Hiltemann avatar Saskia HiltemannNiall Beard avatar Niall Beardorcid logoMateo Boudet avatar Mateo BoudetEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeil

Funding

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

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