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 (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.

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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

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Contributors

This material was contributed to by:

orcid logoHelena Rasche avatar Helena Rascheorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoBérénice Batut avatar Bérénice BatutBazante Sanders avatar Bazante SandersWilliam Durand avatar William DurandNiall Beard avatar Niall Beardorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMaria Doyle avatar Maria Doyleorcid logoLaura Leroi avatar Laura Leroiorcid logoErwan Corre avatar Erwan Correorcid logoAnthony Bretaudeau avatar Anthony BretaudeauKenji Fujihara avatar Kenji FujiharaJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoPaul Zierep avatar Paul ZierepAnton Nekrutenko avatar Anton NekrutenkoEkaterina Polkh avatar Ekaterina PolkhValentin Loux avatar Valentin Louxorcid logoSimon Gladman avatar Simon GladmanEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoSaskia Hiltemann avatar Saskia HiltemannSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoDeepti Varshney avatar Deepti VarshneyGildas Le Corguillé avatar Gildas Le Corguilléorcid logoCristóbal Gallardo avatar Cristóbal GallardoHélène Chiapello avatar Hélène Chiapelloorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMiaomiao Zhou avatar Miaomiao ZhouNathan Dunn avatar Nathan Dunnorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoAnna Syme avatar Anna Symeorcid logoRomane LIBOUBAN avatar Romane LIBOUBANGuillaume Gautreau avatar Guillaume GautreauTwishi Gulati avatar Twishi Gulatiorcid logoBjörn Grüning avatar Björn GrüningTorsten Seemann avatar Torsten Seemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoTeresa Müller avatar Teresa Müller

Funding

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