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
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:

Ekaterina Polkh avatar Ekaterina Polkhorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti VarshneyKenji Fujihara avatar Kenji Fujiharaorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa Müllerorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoSimon Gladman avatar Simon Gladmanorcid logoErwan Corre avatar Erwan CorreEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilNiall Beard avatar Niall Beardorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoStéphanie Robin avatar Stéphanie RobinHélène Chiapello avatar Hélène ChiapelloGuillaume Gautreau avatar Guillaume GautreauValentin Loux avatar Valentin Louxorcid logoMaria Doyle avatar Maria Doyleorcid logoPaul Zierep avatar Paul ZierepNathan Dunn avatar Nathan Dunnorcid logoLaura Leroi avatar Laura LeroiGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnthony Bretaudeau avatar Anthony BretaudeauWilliam Durand avatar William Durandorcid logoSaskia Hiltemann avatar Saskia HiltemannJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoNicola Soranzo avatar Nicola SoranzoSimon Bray avatar Simon Brayorcid logoAnna Syme avatar Anna SymeTorsten Seemann avatar Torsten Seemannorcid logoRomane LIBOUBAN avatar Romane LIBOUBANAnton Nekrutenko avatar Anton NekrutenkoBazante Sanders avatar Bazante SandersTwishi Gulati avatar Twishi Gulati

Funding

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

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ABRomics
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ELIXIR Europe
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IFB
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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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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.