SARS-CoV-2
Tutorials covering analysis of SARS-CoV-2 (COVID 19)
For any question or discussions related to this topic, or to connect with others in the community, please visit the community chat:
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 |
|---|---|---|---|---|---|
| Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads |
Computational chemistry
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring |
Using Galaxy and Managing your Data
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Automating Galaxy workflows using the command line | |||||
| SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis | |||||
| Submitting sequence data to ENA |
Sequence analysis
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Removal of human reads from SARS-CoV-2 sequencing data | |||||
| SARS-CoV-2 Viral Sample Alignment and Variant Visualization |
Variant Analysis
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis | |||||
| Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data |
Editorial Board
This material is reviewed by our Editorial Board:
Wolfgang Maier
Contributors
This material was contributed to by:
Simon Bray
Jasper Ouwerkerk
Robert Meller
Miguel Roncoroni
Mélanie Petera
Adelaide Rhodes
Candace Savonen
Ava Hoffman
Nicola Soranzo
Frederick Tan
Teresa Müller
Katherine Cox
Gildas Le Corguillé
Boris Depoortere
Helena Rasche
Marius van den Beek
Bert Droesbeke
Martin Čech
Beatriz Serrano-Solano
Björn Grüning
Anthony Bretaudeau
Daniel Blankenberg
Wolfgang Maier
Jon Trow
Natalie Kucher
Elizabeth Humphries
Dave Clements
Anton Nekrutenko
Bérénice Batut
Saskia Hiltemann
Armin Dadras
Funding
These individuals or organisations provided funding support for the development of this resource
NHGRI GDS Community Network
BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.
This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)
de.NBI
UFR
ELIXIR-CONVERGE
ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement № 871075
ELIXIR Europe
NHGRI ANVIL
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.