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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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:

Ekaterina Polkh avatar Ekaterina Polkhorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnna Syme avatar Anna Symeorcid logoTeresa Müller avatar Teresa MüllerValentin Loux avatar Valentin LouxAnton Nekrutenko avatar Anton Nekrutenkoorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoPaul Zierep avatar Paul ZierepNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine LariviereGuillaume Gautreau avatar Guillaume Gautreauorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoSimon Gladman avatar Simon GladmanTorsten Seemann avatar Torsten Seemannorcid logoBjörn Grüning avatar Björn GrüningNathan Dunn avatar Nathan Dunnorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoMateo Boudet avatar Mateo BoudetKenji Fujihara avatar Kenji Fujiharaorcid logoSaskia Hiltemann avatar Saskia HiltemannHélène Chiapello avatar Hélène Chiapelloorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSaim Momin avatar Saim MominWilliam Durand avatar William DurandBazante Sanders avatar Bazante Sandersorcid logoAnika Erxleben avatar Anika ErxlebenJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoHelena Rasche avatar Helena Rascheorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon Brayorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoStéphanie Robin avatar Stéphanie RobinTwishi Gulati avatar Twishi Gulatiorcid logoNiklas Mayle avatar Niklas Mayle

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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ELIXIR Europe
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Australian BioCommons
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Melbourne Bioinformatics
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Avans
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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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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.