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 biodiversity
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
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

Contributors

This material was contributed to by:

Kenji Fujihara avatar Kenji Fujiharaorcid logoPaul Zierep avatar Paul ZierepSimon Bray avatar Simon BrayValentin Loux avatar Valentin LouxWilliam Durand avatar William DurandAnton Nekrutenko avatar Anton NekrutenkoNiall Beard avatar Niall Beardorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoHelena Rasche avatar Helena Rascheorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiGuillaume Gautreau avatar Guillaume Gautreauorcid logoJonathan Kreplak avatar Jonathan KreplakTwishi Gulati avatar Twishi Gulatiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo BoudetEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoAnna Syme avatar Anna Symeorcid logoRomane LIBOUBAN avatar Romane LIBOUBANTorsten Seemann avatar Torsten Seemannorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBjörn Grüning avatar Björn GrüningEkaterina Polkh avatar Ekaterina PolkhNathan Dunn avatar Nathan Dunnorcid logoErwan Corre avatar Erwan CorreJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoNicola Soranzo avatar Nicola SoranzoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria DoyleHélène Chiapello avatar Hélène ChiapelloBazante Sanders avatar Bazante Sanders

Funding

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

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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
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IFB
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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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Avans
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ELIXIR Europe