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:

orcid logoWolfgang Maier avatar 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:

Katherine Cox avatar Katherine CoxMarius van den Beek avatar Marius van den BeekFrederick Tan avatar Frederick TanElizabeth Humphries avatar Elizabeth HumphriesCandace Savonen avatar Candace SavonenBoris Depoortere avatar Boris Depoortereorcid logoBert Droesbeke avatar Bert DroesbekeAdelaide Rhodes avatar Adelaide RhodesMiguel Roncoroni avatar Miguel RoncoroniAnton Nekrutenko avatar Anton NekrutenkoRobert Meller avatar Robert MellerNatalie Kucher avatar Natalie Kucherorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon Brayorcid logoDave Clements avatar Dave Clementsorcid logoDaniel Blankenberg avatar Daniel BlankenbergJon Trow avatar Jon TrowAva Hoffman avatar Ava Hoffmanorcid logoWolfgang Maier avatar Wolfgang Maier

Funding

These individuals or organisations provided funding support for the development of this resource