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:

Anton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoTristan Reynolds avatar Tristan ReynoldsGildas Le Corguillé avatar Gildas Le Corguilléorcid logoTeresa Müller avatar Teresa MüllerGuillaume Gautreau avatar Guillaume Gautreauorcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn Grüningorcid logoCristóbal Gallardo avatar Cristóbal GallardoNiall Beard avatar Niall Beardorcid logoAnna Syme avatar Anna SymeTwishi Gulati avatar Twishi Gulatiorcid logoSaskia Hiltemann avatar Saskia HiltemannNathan Dunn avatar Nathan Dunnorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMateo Boudet avatar Mateo Boudetorcid logoRomane LIBOUBAN avatar Romane LIBOUBANWilliam Durand avatar William DurandHélène Chiapello avatar Hélène Chiapelloorcid logoAnika Erxleben avatar Anika ErxlebenKenji Fujihara avatar Kenji Fujiharaorcid logoMaria Doyle avatar Maria Doyleorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoFelicitas Kindel avatar Felicitas KindelValentin Loux avatar Valentin Louxorcid logoPaul Zierep avatar Paul Ziereporcid logoBérénice Batut avatar Bérénice Batutorcid logoErwan Corre avatar Erwan CorreSimon Bray avatar Simon BrayEkaterina Polkh avatar Ekaterina PolkhJasper Ouwerkerk avatar Jasper OuwerkerkEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilTorsten Seemann avatar Torsten Seemannorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSimon Gladman avatar Simon Gladman

Funding

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

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