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
Hands-on: Hands-on: Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

Computational chemistry

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: 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
Hands-on: Hands-on: Automating Galaxy workflows using the command line
Hands-on: Hands-on: SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
Hands-on: Hands-on: Submitting sequence data to ENA

Sequence analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Removal of human reads from SARS-CoV-2 sequencing data
Hands-on: Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization

Variant Analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
Hands-on: Hands-on: 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:

Jon Trow avatar Jon TrowNatalie Kucher avatar Natalie KucherMarius van den Beek avatar Marius van den Beekorcid logoDaniel Blankenberg avatar Daniel BlankenbergElizabeth Humphries avatar Elizabeth HumphriesMiguel Roncoroni avatar Miguel RoncoroniAdelaide Rhodes avatar Adelaide Rhodesorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon BrayKatherine Cox avatar Katherine CoxAva Hoffman avatar Ava Hoffmanorcid logoDave Clements avatar Dave ClementsAnton Nekrutenko avatar Anton Nekrutenkoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBert Droesbeke avatar Bert DroesbekeRobert Meller avatar Robert MellerFrederick Tan avatar Frederick TanCandace Savonen avatar Candace Savonen

Funders

This material was funded by:

ELIXIR-CONVERGE avatar ELIXIR-CONVERGENational Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space avatar NHGRI ANVILBeYond-COVID avatar BeYond-COVIDNational Human Genome Research Institute Genomic Data Science Community Network avatar NHGRI GDS Community Network