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