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:

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Contributors

This material was contributed to by:

orcid logoMateo Boudet avatar Mateo BoudetTorsten Seemann avatar Torsten Seemannorcid logoBérénice Batut avatar Bérénice BatutValentin Loux avatar Valentin Louxorcid logoRomane LIBOUBAN avatar Romane LIBOUBANGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnna Syme avatar Anna SymeWilliam Durand avatar William Durandorcid logoPaul Zierep avatar Paul ZierepGuillaume Gautreau avatar Guillaume Gautreauorcid logoAnika Erxleben avatar Anika ErxlebenJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoHelena Rasche avatar Helena RascheNathan Dunn avatar Nathan Dunnorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon GladmanTwishi Gulati avatar Twishi Gulatiorcid logoLaura Leroi avatar Laura Leroiorcid logoMaria Doyle avatar Maria Doyleorcid logoErwan Corre avatar Erwan CorreEkaterina Polkh avatar Ekaterina PolkhBazante Sanders avatar Bazante Sandersorcid logoMiaomiao Zhou avatar Miaomiao ZhouKenji Fujihara avatar Kenji FujiharaHélène Chiapello avatar Hélène ChiapelloNiall Beard avatar Niall Beardorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoTeresa Müller avatar Teresa Müllerorcid logoFelicitas Kindel avatar Felicitas KindelAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningSimon Bray avatar Simon Brayorcid logoAnthony Bretaudeau avatar Anthony BretaudeauEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoDeepti Varshney avatar Deepti Varshney

Funding

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