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 logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBjörn Grüning avatar Björn Grüningorcid logoMateo Boudet avatar Mateo Boudetorcid logoDeepti Varshney avatar Deepti VarshneyKenji Fujihara avatar Kenji Fujiharaorcid logoJonathan Kreplak avatar Jonathan KreplakSimon Bray avatar Simon BrayJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoAnthony Bretaudeau avatar Anthony BretaudeauAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine LariviereGildas Le Corguillé avatar Gildas Le Corguilléorcid logoPaul Zierep avatar Paul ZierepEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSaskia Hiltemann avatar Saskia HiltemannValentin Loux avatar Valentin LouxNathan Dunn avatar Nathan Dunnorcid logoBérénice Batut avatar Bérénice Batutorcid logoErwan Corre avatar Erwan CorreTwishi Gulati avatar Twishi Gulatiorcid logoMaria Doyle avatar Maria DoyleTorsten Seemann avatar Torsten Seemannorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre CormierWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola SoranzoHélène Chiapello avatar Hélène ChiapelloEkaterina Polkh avatar Ekaterina Polkhorcid logoLaura Leroi avatar Laura Leroiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoHelena Rasche avatar Helena Rascheorcid logoStéphanie Robin avatar Stéphanie RobinBazante Sanders avatar Bazante SandersNiall Beard avatar Niall Beardorcid logoAnna Syme avatar Anna Symeorcid logoAnika Erxleben avatar Anika ErxlebenGuillaume Gautreau avatar Guillaume Gautreauorcid logoSimon Gladman avatar Simon Gladman

Funding

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

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ELIXIR Europe
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IFB
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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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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.