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 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
Genome annotation with Helixer
eukaryota helixer jbrowse1
Masking repeats with RepeatMasker
eukaryote
Genome annotation with Funannotate
gmod eukaryote jbrowse1
Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Genome annotation with Maker
gmod eukaryote jbrowse1 maker
Functional annotation of protein sequences
eukaryote
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2
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

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:

Jasper Ouwerkerk avatar Jasper OuwerkerkEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoPaul Zierep avatar Paul Ziereporcid logoMaria Doyle avatar Maria DoyleSimon Bray avatar Simon BrayGuillaume Gautreau avatar Guillaume Gautreauorcid logoStéphanie Robin avatar Stéphanie RobinKenji Fujihara avatar Kenji Fujiharaorcid logoSaskia Hiltemann avatar Saskia HiltemannNiall Beard avatar Niall Beardorcid logoSimon Gladman avatar Simon GladmanHélène Chiapello avatar Hélène Chiapelloorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningWilliam Durand avatar William Durandorcid logoAnika Erxleben avatar Anika ErxlebenEkaterina Polkh avatar Ekaterina Polkhorcid logoCristóbal Gallardo avatar Cristóbal GallardoTwishi Gulati avatar Twishi Gulatiorcid logoBérénice Batut avatar Bérénice Batutorcid logoRomane LIBOUBAN avatar Romane LIBOUBANAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLaura Leroi avatar Laura Leroiorcid logoDelphine Lariviere avatar Delphine LariviereValentin Loux avatar Valentin LouxTorsten Seemann avatar Torsten Seemannorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena Rascheorcid logoMiaomiao Zhou avatar Miaomiao ZhouGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti VarshneyNathan Dunn avatar Nathan Dunnorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoAnna Syme avatar Anna Syme

Funding

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

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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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ABRomics
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Avans
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ELIXIR Europe
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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.