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:

Bazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan KreplakEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilHélène Chiapello avatar Hélène Chiapelloorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti VarshneyKenji Fujihara avatar Kenji FujiharaTwishi Gulati avatar Twishi Gulatiorcid logoTristan Reynolds avatar Tristan ReynoldsGuillaume Gautreau avatar Guillaume Gautreauorcid logoPaul Zierep avatar Paul ZierepEkaterina Polkh avatar Ekaterina Polkhorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMateo Boudet avatar Mateo BoudetAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoTeresa Müller avatar Teresa Müllerorcid logoErwan Corre avatar Erwan Correorcid logoBjörn Grüning avatar Björn Grüningorcid logoNiklas Mayle avatar Niklas Mayleorcid logoRomane LIBOUBAN avatar Romane LIBOUBANValentin Loux avatar Valentin Louxorcid logoMaria Doyle avatar Maria Doyleorcid logoAnna Syme avatar Anna Symeorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaim Momin avatar Saim MominGildas Le Corguillé avatar Gildas Le CorguilléNathan Dunn avatar Nathan DunnNiall Beard avatar Niall BeardJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoCristóbal Gallardo avatar Cristóbal GallardoTorsten Seemann avatar Torsten Seemannorcid logoHelena Rasche avatar Helena Rascheorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoLaura Leroi avatar Laura Leroiorcid logoAnika Erxleben avatar Anika ErxlebenSimon Bray avatar Simon Brayorcid logoSimon Gladman avatar Simon Gladmanorcid logoMiaomiao Zhou avatar Miaomiao ZhouWilliam Durand avatar William Durandorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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

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Melbourne Bioinformatics
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The University of Melbourne
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ELIXIR Europe
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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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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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ABRomics
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IFB
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Avans