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