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:
Ava Hoffman
Nicola Soranzo
Daniel Blankenberg
Jon Trow
Elizabeth Humphries
Wolfgang Maier
Björn Grüning
Miguel Roncoroni
Anton Nekrutenko
Boris Depoortere
Helena Rasche
Simon Bray
Adelaide Rhodes
Gildas Le Corguillé
Saskia Hiltemann
Anthony Bretaudeau
Marius van den Beek
Dave Clements
Katherine Cox
Mélanie Petera
Candace Savonen
Armin Dadras
Bérénice Batut
Frederick Tan
Natalie Kucher
Jasper Ouwerkerk
Beatriz Serrano-Solano
Teresa Müller
Bert Droesbeke
Martin Čech
Robert Meller
Funding
These individuals or organisations provided funding support for the development of this resource
NHGRI GDS Community Network
NHGRI ANVIL
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)
ELIXIR Europe
UFR
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-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
de.NBI