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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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 logoDeepti Varshney avatar Deepti VarshneyTwishi Gulati avatar Twishi Gulatiorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoFelicitas Kindel avatar Felicitas KindelAnton Nekrutenko avatar Anton NekrutenkoValentin Loux avatar Valentin LouxHélène Chiapello avatar Hélène Chiapelloorcid logoBjörn Grüning avatar Björn Grüningorcid logoRomane LIBOUBAN avatar Romane LIBOUBANNathan Dunn avatar Nathan Dunnorcid logoLaura Leroi avatar Laura Leroiorcid logoSimon Gladman avatar Simon GladmanGuillaume Gautreau avatar Guillaume GautreauTorsten Seemann avatar Torsten Seemannorcid logoAnna Syme avatar Anna Symeorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPaul Zierep avatar Paul ZierepEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoCristóbal Gallardo avatar Cristóbal GallardoNiall Beard avatar Niall BeardSimon Bray avatar Simon Brayorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoJonathan Kreplak avatar Jonathan KreplakBazante Sanders avatar Bazante SandersKenji Fujihara avatar Kenji FujiharaJasper Ouwerkerk avatar Jasper OuwerkerkWilliam Durand avatar William DurandEkaterina Polkh avatar Ekaterina Polkhorcid logoMateo Boudet avatar Mateo Boudetorcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHelena Rasche avatar Helena Rasche

Funding

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