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:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

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Contributors

This material was contributed to by:

orcid logoJonathan Kreplak avatar Jonathan KreplakNathan Dunn avatar Nathan Dunnorcid logoTeresa Müller avatar Teresa MüllerEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoAlexandre Cormier avatar Alexandre CormierGuillaume Gautreau avatar Guillaume Gautreauorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoFelicitas Kindel avatar Felicitas KindelGildas Le Corguillé avatar Gildas Le CorguilléNiall Beard avatar Niall Beardorcid logoLaura Leroi avatar Laura LeroiJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoErwan Corre avatar Erwan Correorcid logoPaul Zierep avatar Paul ZierepValentin Loux avatar Valentin LouxAnton Nekrutenko avatar Anton NekrutenkoWilliam Durand avatar William DurandTorsten Seemann avatar Torsten Seemannorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSimon Gladman avatar Simon Gladmanorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoMaria Doyle avatar Maria DoyleHélène Chiapello avatar Hélène Chiapelloorcid logoBjörn Grüning avatar Björn GrüningEkaterina Polkh avatar Ekaterina Polkhorcid logoMateo Boudet avatar Mateo Boudetorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoSaskia Hiltemann avatar Saskia HiltemannBazante Sanders avatar Bazante SandersTwishi Gulati avatar Twishi Gulatiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnna Syme avatar Anna Symeorcid logoAnika Erxleben avatar Anika ErxlebenKenji Fujihara avatar Kenji Fujiharaorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon Bray

Funding

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