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:

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Contributors

This material was contributed to by:

Jasper Ouwerkerk avatar Jasper OuwerkerkEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoPaul Zierep avatar Paul Ziereporcid logoMaria Doyle avatar Maria DoyleSimon Bray avatar Simon BrayGuillaume Gautreau avatar Guillaume Gautreauorcid logoStéphanie Robin avatar Stéphanie RobinKenji Fujihara avatar Kenji Fujiharaorcid logoSaskia Hiltemann avatar Saskia HiltemannNiall Beard avatar Niall Beardorcid logoSimon Gladman avatar Simon GladmanHélène Chiapello avatar Hélène Chiapelloorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningWilliam Durand avatar William Durandorcid logoAnika Erxleben avatar Anika ErxlebenEkaterina Polkh avatar Ekaterina Polkhorcid logoCristóbal Gallardo avatar Cristóbal GallardoTwishi Gulati avatar Twishi Gulatiorcid logoBérénice Batut avatar Bérénice Batutorcid logoRomane LIBOUBAN avatar Romane LIBOUBANAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLaura Leroi avatar Laura Leroiorcid logoDelphine Lariviere avatar Delphine LariviereValentin Loux avatar Valentin LouxTorsten Seemann avatar Torsten Seemannorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena Rascheorcid logoMiaomiao Zhou avatar Miaomiao ZhouGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti VarshneyNathan Dunn avatar Nathan Dunnorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoAnna Syme avatar Anna Syme

Funding

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