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.
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Requirements
Before diving into this topic, we recommend you to have a look at:
Material
Introduction
Start here if you are new to genome annotation in Galaxy.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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Introduction to Genome Annotation
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Prokaryotes
Annotation of prokaryotic genomes.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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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.
Other
Assorted Tutorials
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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From small to large-scale genome comparison
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Comparative gene analysis in unannotated genomes |
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/genome-annotation-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
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:
Helena Rasche Simon Gladman Anthony BretaudeauFor any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Helena Rasche Mateo Boudet Torsten Seemann Erwan Corre Anthony Bretaudeau Saskia Hiltemann Kenji Fujihara Delphine Lariviere Miaomiao Zhou Stéphanie Robin Jonathan Kreplak Esteban Perez-Wohlfeil Bérénice Batut Paul Zierep Björn Grüning Twishi Gulati Anna Syme Alexandre Cormier Simon Gladman Anton Nekrutenko Avans Hogeschool Anika Erxleben Maria Doyle Bazante Sanders Laura Leroi Nathan DunnFunders
This material was funded by:
ABRomics Gallantries EuroScienceGateway