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:

comment   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 (slides) and tutorial (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
Genome annotation with Prokka
Identification of AMR genes in an assembled bacterial genome
Refining Genome Annotations with Apollo (prokaryotes)
Essential genes detection with Transposon insertion sequencing

Eukaryotes

Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Comparison of two annotation tools - Helixer and Braker3
Genome annotation with Braker3
Genome annotation with Helixer
Masking repeats with RepeatMasker
Genome annotation with Funannotate
Genome annotation with Maker (short)
Genome annotation with Maker
Functional annotation of protein sequences
Refining Genome Annotations with Apollo (eukaryotes)
Long non-coding RNAs (lncRNAs) annotation with FEELnc
CRISPR screen analysis

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
From small to large-scale genome comparison
Comparative gene analysis in unannotated genomes

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 rss-feed 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:

Esteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilBazante Sanders avatar Bazante Sandersorcid logoPaul Zierep avatar Paul Ziereporcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le CorguilléJasper Ouwerkerk avatar Jasper OuwerkerkTwishi Gulati avatar Twishi Gulatiorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William Durandorcid logoJonathan Kreplak avatar Jonathan KreplakHélène Chiapello avatar Hélène Chiapelloorcid logoLaura Leroi avatar Laura Leroiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnika Erxleben avatar Anika ErxlebenTorsten Seemann avatar Torsten SeemannEkaterina Polkh avatar Ekaterina PolkhValentin Loux avatar Valentin Louxorcid logoBjörn Grüning avatar Björn GrüningGuillaume Gautreau avatar Guillaume Gautreauorcid logoAnna Syme avatar Anna SymeNiall Beard avatar Niall BeardKenji Fujihara avatar Kenji FujiharaNathan Dunn avatar Nathan Dunnorcid logoTeresa Müller avatar Teresa Müllerorcid logoMateo Boudet avatar Mateo Boudetorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoStéphanie Robin avatar Stéphanie RobinSimon Bray avatar Simon Brayorcid logoErwan Corre avatar Erwan CorreAnton Nekrutenko avatar Anton Nekrutenkoorcid logoRomane LIBOUBAN avatar Romane LIBOUBAN

Funding

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