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:

Kenji Fujihara avatar Kenji FujiharaHélène Chiapello avatar Hélène Chiapelloorcid logoSaskia Hiltemann avatar Saskia HiltemannGildas Le Corguillé avatar Gildas Le Corguilléorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoRomane LIBOUBAN avatar Romane LIBOUBANTorsten Seemann avatar Torsten Seemannorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnna Syme avatar Anna SymeValentin Loux avatar Valentin Louxorcid logoErwan Corre avatar Erwan Correorcid logoPaul Zierep avatar Paul ZierepNathan Dunn avatar Nathan Dunnorcid logoLaura Leroi avatar Laura Leroiorcid logoTeresa Müller avatar Teresa Müllerorcid logoDeepti Varshney avatar Deepti VarshneyJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William Durandorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnika Erxleben avatar Anika ErxlebenSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNicola Soranzo avatar Nicola SoranzoEkaterina Polkh avatar Ekaterina Polkhorcid logoStéphanie Robin avatar Stéphanie RobinGuillaume Gautreau avatar Guillaume GautreauNiall Beard avatar Niall BeardEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon GladmanBazante Sanders avatar Bazante Sandersorcid logoMateo Boudet avatar Mateo BoudetTwishi Gulati avatar Twishi Gulati

Funding

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