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 () and 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
covid19

Computational chemistry

Lesson Slides Hands-on Recordings Input dataset Workflows
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
covid19 one-health

Using Galaxy and Managing your Data

Lesson Slides Hands-on Recordings Input dataset Workflows
Automating Galaxy workflows using the command line
workflows variant-analysis covid19
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
ncbi covid19
Submitting sequence data to ENA
covid19

Sequence analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Removal of human reads from SARS-CoV-2 sequencing data
covid19
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19

Variant Analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
covid19 virology one-health
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
covid19 virology one-health

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 logoAvatarWolfgang 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:

AvatarMiguel RoncoroniAvatarNatalie KucherAvatarElizabeth HumphriesAvatarCandace SavonenAvatarSimon BrayAvatarAnton NekrutenkoAvatarJon Troworcid logoAvatarDaniel BlankenbergAvatarFrederick TanAvatarAva Hoffmanorcid logoAvatarBérénice Batutorcid logoAvatarDave ClementsAvatarAdelaide RhodesAvatarMarius van den BeekAvatarRobert MellerAvatarKatherine Coxorcid logoAvatarWolfgang Maierorcid logoAvatarBert Droesbeke

Funders

This material was funded by:

AvatarBeYond-COVIDAvatarELIXIR-CONVERGEAvatarNational Human Genome Research Institute Genomic Data Science Community NetworkAvatarNational Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space