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 logoPaul Zierep avatar Paul ZierepWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal GallardoNiall Beard avatar Niall Beardorcid logoSimon Gladman avatar Simon GladmanGildas Le Corguillé avatar Gildas Le Corguilléorcid logoDelphine Lariviere avatar Delphine LariviereValentin Loux avatar Valentin Louxorcid logoBjörn Grüning avatar Björn Grüningorcid logoTeresa Müller avatar Teresa Müllerorcid logoSaskia Hiltemann avatar Saskia HiltemannNathan Dunn avatar Nathan Dunnorcid logoErwan Corre avatar Erwan CorreBazante Sanders avatar Bazante Sandersorcid logoBérénice Batut avatar Bérénice Batutorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoJonathan Kreplak avatar Jonathan KreplakGuillaume Gautreau avatar Guillaume GautreauJasper Ouwerkerk avatar Jasper OuwerkerkEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilTwishi Gulati avatar Twishi Gulatiorcid logoDeepti Varshney avatar Deepti VarshneySimon Bray avatar Simon BrayKenji Fujihara avatar Kenji Fujiharaorcid logoHelena Rasche avatar Helena Rascheorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMaria Doyle avatar Maria Doyleorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauTorsten Seemann avatar Torsten SeemannHélène Chiapello avatar Hélène Chiapelloorcid logoRomane LIBOUBAN avatar Romane LIBOUBANEkaterina Polkh avatar Ekaterina Polkhorcid logoAnna Syme avatar Anna Symeorcid logoMateo Boudet avatar Mateo Boudet

Funding

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