SARS-CoV-2
Tutorials covering analysis of SARS-CoV-2 (COVID 19)
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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:
Wolfgang Maier
Simon Bray
Anton Nekrutenko
Bérénice Batut
Ava Hoffman
Beatriz Serrano-Solano
Daniel Blankenberg
Jon Trow
Armin Dadras
Martin Čech
Miguel Roncoroni
Bert Droesbeke
Dave Clements
Teresa Müller
Björn Grüning
Katherine Cox
Anthony Bretaudeau
Nicola Soranzo
Robert Meller
Marius van den Beek
Natalie Kucher
Mélanie Petera
Frederick Tan
Helena Rasche
Gildas Le Corguillé
Jasper Ouwerkerk
Saskia Hiltemann
Candace Savonen
Adelaide Rhodes
Boris Depoortere
Elizabeth Humphries
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)
UFR
NHGRI ANVIL
de.NBI
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.
ELIXIR Europe
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