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 |
|---|---|---|---|---|---|
| From small to large-scale genome comparison | |||||
| Genome annotation with Prokka | |||||
| Pangenome analysis with Roary | |||||
| Refining Genome Annotations with Apollo (prokaryotes) | |||||
| Comparative gene analysis in unannotated genomes |
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:
Helena Rasche
Daniela Brites
Mélanie Petera
Esteban Perez-Wohlfeil
Stéphanie Robin
Maria Doyle
Ekaterina Polkh
Saim Momin
Tristan Reynolds
Nathan Dunn
Niall Beard
Peter van Heusden
Gildas Le Corguillé
Anika Erxleben
Björn Grüning
Enis Afgan
Lucille Delisle
Simon Gladman
Nicola Soranzo
Simon Bray
Wolfgang Maier
Niklas Mayle
Saskia Hiltemann
Delphine Lariviere
Thoba Lose
Galo A. Goig
Christoph Stritt
Anna Syme
Alex Ostrovsky
Torsten Seemann
Jennifer Hillman-Jackson
William Durand
Cristóbal Gallardo
Anthony Bretaudeau
Anton Nekrutenko
Linelle Abueg
Mateo Boudet
Bérénice Batut
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
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.
The University of Melbourne
Australian BioCommons
Melbourne Bioinformatics