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
Essential genes detection with Transposon insertion sequencing
bacteria tnseq essential genes microgalaxy
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

Eukaryotes

Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
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
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

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy biodiversity
From small to large-scale genome comparison
plants prokaryote
Pangenome analysis with Roary
pangenome prokaryote phylogeny

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

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Contributors

This material was contributed to by:

orcid logoTeresa Müller avatar Teresa MüllerWilliam Durand avatar William DurandEkaterina Polkh avatar Ekaterina Polkhorcid logoAnna Syme avatar Anna Symeorcid logoRomane LIBOUBAN avatar Romane LIBOUBANNiall Beard avatar Niall Beardorcid logoNiklas Mayle avatar Niklas MayleNathan Dunn avatar Nathan Dunnorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPaul Zierep avatar Paul Ziereporcid logoMiaomiao Zhou avatar Miaomiao ZhouHélène Chiapello avatar Hélène ChiapelloBazante Sanders avatar Bazante SandersValentin Loux avatar Valentin Louxorcid logoHelena Rasche avatar Helena RascheKenji Fujihara avatar Kenji FujiharaAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoSimon Gladman avatar Simon Gladmanorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnthony Bretaudeau avatar Anthony BretaudeauGuillaume Gautreau avatar Guillaume Gautreauorcid logoDeepti Varshney avatar Deepti VarshneyEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoLaura Leroi avatar Laura Leroiorcid logoMaria Doyle avatar Maria Doyleorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnika Erxleben avatar Anika ErxlebenJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoSaim Momin avatar Saim MominSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo Boudetorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSaskia Hiltemann avatar Saskia HiltemannGildas Le Corguillé avatar Gildas Le CorguilléTorsten Seemann avatar Torsten Seemannorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoErwan Corre avatar Erwan CorreTwishi Gulati avatar Twishi Gulatiorcid logoJonathan Kreplak avatar Jonathan Kreplak

Funding

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

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ELIXIR Europe
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Avans
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Australian BioCommons
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The University of Melbourne
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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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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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Melbourne Bioinformatics
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IFB