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
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.

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 logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMiaomiao Zhou avatar Miaomiao ZhouTorsten Seemann avatar Torsten Seemannorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoHelena Rasche avatar Helena Rascheorcid logoMaria Doyle avatar Maria DoyleKenji Fujihara avatar Kenji Fujiharaorcid logoMateo Boudet avatar Mateo Boudetorcid logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti Varshneyorcid logoAnika Erxleben avatar Anika ErxlebenHélène Chiapello avatar Hélène Chiapelloorcid logoSimon Gladman avatar Simon GladmanWilliam Durand avatar William DurandAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoErwan Corre avatar Erwan Correorcid logoAnna Syme avatar Anna Symeorcid logoBérénice Batut avatar Bérénice BatutJasper Ouwerkerk avatar Jasper OuwerkerkGuillaume Gautreau avatar Guillaume Gautreauorcid logoNicola Soranzo avatar Nicola SoranzoValentin Loux avatar Valentin Louxorcid logoDelphine Lariviere avatar Delphine LariviereNathan Dunn avatar Nathan Dunnorcid logoLaura Leroi avatar Laura LeroiTwishi Gulati avatar Twishi Gulatiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia HiltemannEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoAlexandre Cormier avatar Alexandre CormierBazante Sanders avatar Bazante Sandersorcid logoTeresa Müller avatar Teresa MüllerNiall Beard avatar Niall BeardSimon Bray avatar Simon BrayGildas Le Corguillé avatar Gildas Le CorguilléEkaterina Polkh avatar Ekaterina Polkhorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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

Logo
IFB
Logo
ABRomics
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
ELIXIR Europe
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.