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:

Guillaume Gautreau avatar Guillaume Gautreauorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoHelena Rasche avatar Helena RascheBazante Sanders avatar Bazante Sandersorcid logoSimon Gladman avatar Simon GladmanWilliam Durand avatar William DurandGildas Le Corguillé avatar Gildas Le CorguilléSimon Bray avatar Simon BrayAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNathan Dunn avatar Nathan Dunnorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoPaul Zierep avatar Paul ZierepKenji Fujihara avatar Kenji Fujiharaorcid logoErwan Corre avatar Erwan Correorcid logoLaura Leroi avatar Laura Leroiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo Boudetorcid logoRomane LIBOUBAN avatar Romane LIBOUBANTwishi Gulati avatar Twishi Gulatiorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMaria Doyle avatar Maria Doyleorcid logoAnna Syme avatar Anna SymeEkaterina Polkh avatar Ekaterina PolkhHélène Chiapello avatar Hélène ChiapelloTorsten Seemann avatar Torsten Seemannorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoValentin Loux avatar Valentin Louxorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoBjörn Grüning avatar Björn Grüningorcid logoTeresa Müller avatar Teresa Müllerorcid logoJonathan Kreplak avatar Jonathan KreplakNiall Beard avatar Niall Beardorcid logoAnika Erxleben avatar Anika ErxlebenEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAlexandre Cormier avatar Alexandre Cormier

Funding

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