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 logoJonathan Kreplak avatar Jonathan KreplakEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilBazante Sanders avatar Bazante Sandersorcid logoPaul Zierep avatar Paul ZierepValentin Loux avatar Valentin Louxorcid logoHelena Rasche avatar Helena RascheWilliam Durand avatar William Durandorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBérénice Batut avatar Bérénice BatutGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnna Syme avatar Anna SymeJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoBjörn Grüning avatar Björn GrüningSimon Bray avatar Simon Brayorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoTeresa Müller avatar Teresa MüllerTorsten Seemann avatar Torsten SeemannTwishi Gulati avatar Twishi GulatiEkaterina Polkh avatar Ekaterina Polkhorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoMaria Doyle avatar Maria DoyleNathan Dunn avatar Nathan Dunnorcid logoSimon Gladman avatar Simon GladmanKenji Fujihara avatar Kenji Fujiharaorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANHélène Chiapello avatar Hélène Chiapelloorcid logoErwan Corre avatar Erwan Correorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal GallardoGuillaume Gautreau avatar Guillaume Gautreauorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoLaura Leroi avatar Laura LeroiNiall Beard avatar Niall Beard

Funding

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