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
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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Editorial Board

This material is reviewed by our Editorial Board:

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Contributors

This material was contributed to by:

orcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa MüllerHélène Chiapello avatar Hélène ChiapelloJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoPaul Zierep avatar Paul ZierepWilliam Durand avatar William Durandorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnna Syme avatar Anna Symeorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoLaura Leroi avatar Laura Leroiorcid logoAnika Erxleben avatar Anika ErxlebenSimon Bray avatar Simon BrayEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilTwishi Gulati avatar Twishi Gulatiorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia HiltemannBazante Sanders avatar Bazante SandersAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie RobinValentin Loux avatar Valentin LouxKenji Fujihara avatar Kenji FujiharaTorsten Seemann avatar Torsten Seemannorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn Grüningorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoFelicitas Kindel avatar Felicitas KindelNiall Beard avatar Niall BeardGildas Le Corguillé avatar Gildas Le Corguilléorcid logoSimon Gladman avatar Simon Gladmanorcid logoHelena Rasche avatar Helena RascheGuillaume Gautreau avatar Guillaume GautreauNathan Dunn avatar Nathan Dunnorcid logoMaria Doyle avatar Maria DoyleEkaterina Polkh avatar Ekaterina Polkhorcid logoBérénice Batut avatar Bérénice Batut

Funding

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