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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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 logoMaria Doyle avatar Maria DoyleTorsten Seemann avatar Torsten Seemannorcid logoFelicitas Kindel avatar Felicitas KindelValentin Loux avatar Valentin LouxNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnthony Bretaudeau avatar Anthony BretaudeauWilliam Durand avatar William Durandorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoErwan Corre avatar Erwan CorreJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoSimon Gladman avatar Simon GladmanBazante Sanders avatar Bazante Sandersorcid logoNicola Soranzo avatar Nicola SoranzoKenji Fujihara avatar Kenji Fujiharaorcid logoJonathan Kreplak avatar Jonathan KreplakGuillaume Gautreau avatar Guillaume Gautreauorcid logoAnna Syme avatar Anna SymeSimon Bray avatar Simon Brayorcid logoPaul Zierep avatar Paul ZierepHélène Chiapello avatar Hélène Chiapelloorcid logoLaura Leroi avatar Laura LeroiTwishi Gulati avatar Twishi Gulatiorcid logoBérénice Batut avatar Bérénice BatutAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBjörn Grüning avatar Björn Grüningorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal GallardoNathan Dunn avatar Nathan Dunnorcid logoTeresa Müller avatar Teresa MüllerGildas Le Corguillé avatar Gildas Le CorguilléEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoMateo Boudet avatar Mateo Boudet

Funding

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

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ABRomics
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Avans
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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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IFB
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ELIXIR Europe
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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.