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 logoMiaomiao Zhou avatar Miaomiao ZhouValentin Loux avatar Valentin Louxorcid logoErwan Corre avatar Erwan CorreHélène Chiapello avatar Hélène Chiapelloorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauDeepti Varshney avatar Deepti VarshneyKenji Fujihara avatar Kenji FujiharaJasper Ouwerkerk avatar Jasper OuwerkerkTeresa Müller avatar Teresa MüllerGuillaume Gautreau avatar Guillaume Gautreauorcid logoJonathan Kreplak avatar Jonathan KreplakSimon Bray avatar Simon Brayorcid logoLaura Leroi avatar Laura Leroiorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnna Syme avatar Anna SymeEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilEkaterina Polkh avatar Ekaterina PolkhTwishi Gulati avatar Twishi GulatiNathan Dunn avatar Nathan DunnGildas Le Corguillé avatar Gildas Le Corguilléorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSimon Gladman avatar Simon GladmanWilliam Durand avatar William DurandNiall Beard avatar Niall BeardTorsten Seemann avatar Torsten Seemannorcid logoPaul Zierep avatar Paul Ziereporcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoDelphine Lariviere avatar Delphine LariviereAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoMateo Boudet avatar Mateo Boudetorcid logoMaria Doyle avatar Maria DoyleBazante Sanders avatar Bazante Sandersorcid logoFelicitas Kindel avatar Felicitas Kindel

Funding

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