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:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

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Contributors

This material was contributed to by:

orcid logoLaura Leroi avatar Laura LeroiJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAlexandre Cormier avatar Alexandre CormierGuillaume Gautreau avatar Guillaume Gautreauorcid logoMaria Doyle avatar Maria Doyleorcid logoPaul Zierep avatar Paul ZierepGildas Le Corguillé avatar Gildas Le Corguilléorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoBérénice Batut avatar Bérénice BatutHélène Chiapello avatar Hélène Chiapelloorcid logoBjörn Grüning avatar Björn Grüningorcid logoErwan Corre avatar Erwan Correorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNathan Dunn avatar Nathan Dunnorcid logoAnika Erxleben avatar Anika ErxlebenTorsten Seemann avatar Torsten Seemannorcid logoTeresa Müller avatar Teresa MüllerEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilBazante Sanders avatar Bazante Sandersorcid logoAnna Syme avatar Anna Symeorcid logoSimon Gladman avatar Simon Gladmanorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoStéphanie Robin avatar Stéphanie RobinNiall Beard avatar Niall BeardTwishi Gulati avatar Twishi GulatiSimon Bray avatar Simon BrayWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal GallardoValentin Loux avatar Valentin Louxorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoFelicitas Kindel avatar Felicitas KindelEkaterina Polkh avatar Ekaterina Polkhorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoRomane LIBOUBAN avatar Romane LIBOUBANKenji Fujihara avatar Kenji Fujiharaorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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