prokaryote
Tutorials covering prokaryote
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.Assembly
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Making sense of a newly assembled genome | |||||
| Unicycler Assembly |
Evolution
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Identifying tuberculosis transmission links: from SNPs to transmission clusters | |||||
| Tree thinking for tuberculosis evolution and epidemiology |
Genome Annotation
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Comparative gene analysis in unannotated genomes | |||||
| From small to large-scale genome comparison | |||||
| Genome annotation with Prokka | |||||
| Pangenome analysis with Roary | |||||
| Refining Genome Annotations with Apollo (prokaryotes) |
Variant Analysis
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Calling variants in non-diploid systems | |||||
| M. tuberculosis Variant Analysis | |||||
| Microbial Variant Calling |
Contributors
This material was contributed to by:
Thoba Lose
Simon Bray
Mateo Boudet
Daniela Brites
Esteban Perez-Wohlfeil
Christoph Stritt
Mélanie Pétéra
Niall Beard
Björn Grüning
Anika Erxleben
William Durand
Cristóbal Gallardo
Jennifer Hillman-Jackson
Anton Nekrutenko
Lucille Delisle
Saim Momin
Enis Afgan
Saskia Hiltemann
Anna Syme
Alex Ostrovsky
Nicola Soranzo
Niklas Mayle
Bérénice Batut
Delphine Lariviere
Wolfgang Maier
Simon Gladman
Galo A. Goig
Peter van Heusden
Anthony Bretaudeau
Gildas Le Corguillé
Stéphanie Robin
Tristan Reynolds
Maria Doyle
Ekaterina Polkh
Nathan Dunn
Helena Rasche
Torsten Seemann
Linelle Abueg
Funding
These individuals or organisations provided funding support for the development of this resource
Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
ELIXIR Europe
Melbourne Bioinformatics
EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
Australian BioCommons
The University of Melbourne