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.

For any question or discussions related to this topic, or to connect with others in the community, please visit the community chat:

  Community Matrix Chat

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.

Follow topic updates with our RSS Feed

Community Resources

Community Home Maintainer Home

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoSimon Gladman avatar Simon Gladmanorcid logoAnna Syme avatar Anna Symeorcid logoNiklas Mayle avatar Niklas Mayleorcid logoTeresa Müller avatar Teresa Müllerorcid logoMaria Doyle avatar Maria Doyleorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBérénice Batut avatar Bérénice BatutKenji Fujihara avatar Kenji FujiharaBazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoFelicitas Kindel avatar Felicitas KindelSimon Bray avatar Simon BrayEkaterina Polkh avatar Ekaterina PolkhNathan Dunn avatar Nathan Dunnorcid logoErwan Corre avatar Erwan Correorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal GallardoJasper Ouwerkerk avatar Jasper OuwerkerkGuillaume Gautreau avatar Guillaume Gautreauorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaura Leroi avatar Laura LeroiHélène Chiapello avatar Hélène ChiapelloValentin Loux avatar Valentin Louxorcid logoHelena Rasche avatar Helena Rascheorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoPaul Zierep avatar Paul ZierepGildas Le Corguillé avatar Gildas Le CorguilléAnton Nekrutenko avatar Anton Nekrutenkoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANWilliam Durand avatar William Durandorcid logoSaim Momin avatar Saim MominTorsten Seemann avatar Torsten SeemannNiall Beard avatar Niall BeardEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilTwishi Gulati avatar Twishi Gulati

Funding

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

Logo
IFB
Logo
Avans
Logo
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.
Logo
Australian BioCommons
Logo
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.
Logo
ABRomics
Logo
ELIXIR Europe
Logo
Melbourne Bioinformatics
Logo
The University of Melbourne