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:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Contributors

This material was contributed to by:

orcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoRomane LIBOUBAN avatar Romane LIBOUBANEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilValentin Loux avatar Valentin LouxEkaterina Polkh avatar Ekaterina Polkhorcid logoLaura Leroi avatar Laura Leroiorcid logoJonathan Kreplak avatar Jonathan KreplakHélène Chiapello avatar Hélène ChiapelloJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoNicola Soranzo avatar Nicola SoranzoNathan Dunn avatar Nathan DunnAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPaul Zierep avatar Paul Ziereporcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante SandersGildas Le Corguillé avatar Gildas Le CorguilléTorsten Seemann avatar Torsten SeemannTwishi Gulati avatar Twishi GulatiSimon Bray avatar Simon BrayNiall Beard avatar Niall Beardorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoSaskia Hiltemann avatar Saskia HiltemannWilliam Durand avatar William Durandorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSimon Gladman avatar Simon Gladmanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBérénice Batut avatar Bérénice Batutorcid logoHelena Rasche avatar Helena Rascheorcid logoMateo Boudet avatar Mateo Boudetorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoFelicitas Kindel avatar Felicitas KindelKenji Fujihara avatar Kenji Fujiharaorcid logoBjörn Grüning avatar Björn Grüningorcid logoMaria Doyle avatar Maria DoyleGuillaume Gautreau avatar Guillaume Gautreauorcid logoErwan Corre avatar Erwan Correorcid logoTeresa Müller avatar Teresa Müller

Funding

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