SARS-CoV-2
Tutorials covering analysis of SARS-CoV-2 (COVID 19)
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Material
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 |
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
Editorial Board
This material is reviewed by our Editorial Board:
Wolfgang Maier
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Simon Bray
Anton Nekrutenko
Marius van den Beek
Ava Hoffman
Daniel Blankenberg
Dave Clements
Bérénice Batut
Bert Droesbeke
Candace Savonen
Frederick Tan
Adelaide Rhodes
Wolfgang Maier
Natalie Kucher
Miguel Roncoroni
Katherine Cox
Elizabeth Humphries
Boris Depoortere
Robert Meller
Jon Trow
Funding
These individuals or organisations provided funding support for the development of this resource
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-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
NHGRI GDS Community Network