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:

Torsten Seemann avatar Torsten Seemannorcid logoAnika Erxleben avatar Anika ErxlebenWilliam Durand avatar William DurandEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoPaul Zierep avatar Paul Ziereporcid logoSaskia Hiltemann avatar Saskia HiltemannKenji Fujihara avatar Kenji FujiharaTwishi Gulati avatar Twishi Gulatiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMateo Boudet avatar Mateo Boudetorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaura Leroi avatar Laura LeroiGildas Le Corguillé avatar Gildas Le CorguilléHélène Chiapello avatar Hélène Chiapelloorcid logoMaria Doyle avatar Maria Doyleorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAnna Syme avatar Anna Symeorcid logoDelphine Lariviere avatar Delphine LariviereNathan Dunn avatar Nathan Dunnorcid logoBérénice Batut avatar Bérénice BatutEkaterina Polkh avatar Ekaterina Polkhorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDeepti Varshney avatar Deepti VarshneyValentin Loux avatar Valentin Louxorcid logoTeresa Müller avatar Teresa Müllerorcid logoSimon Gladman avatar Simon GladmanSimon Bray avatar Simon Brayorcid logoFelicitas Kindel avatar Felicitas KindelGuillaume Gautreau avatar Guillaume GautreauJasper Ouwerkerk avatar Jasper OuwerkerkBazante Sanders avatar Bazante Sandersorcid logoAlexandre Cormier avatar Alexandre CormierNiall Beard avatar Niall BeardAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoErwan Corre avatar Erwan Corre

Funding

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

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ABRomics
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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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IFB
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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.