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:

orcid logoMateo Boudet avatar Mateo Boudetorcid logoMaria Doyle avatar Maria DoyleWilliam Durand avatar William Durandorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola SoranzoNathan Dunn avatar Nathan DunnAnton Nekrutenko avatar Anton NekrutenkoEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilHélène Chiapello avatar Hélène ChiapelloSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn GrüningTorsten Seemann avatar Torsten Seemannorcid logoBérénice Batut avatar Bérénice BatutGuillaume Gautreau avatar Guillaume GautreauGildas Le Corguillé avatar Gildas Le CorguilléValentin Loux avatar Valentin LouxNiall Beard avatar Niall Beardorcid logoHelena Rasche avatar Helena Rascheorcid logoTeresa Müller avatar Teresa Müllerorcid logoSimon Gladman avatar Simon Gladmanorcid logoPaul Zierep avatar Paul ZierepTwishi Gulati avatar Twishi Gulatiorcid logoStéphanie Robin avatar Stéphanie RobinJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAnna Syme avatar Anna Symeorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan CorreKenji Fujihara avatar Kenji Fujiharaorcid logoLaura Leroi avatar Laura LeroiEkaterina Polkh avatar Ekaterina Polkhorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoRomane LIBOUBAN avatar Romane LIBOUBAN

Funding

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

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Avans
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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.
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ABRomics
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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.