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

Sequence analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Removal of human reads from SARS-CoV-2 sequencing data
covid19
Hands-on: Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1

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
covid19 virology one-health
Hands-on: Hands-on: 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 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 TrowAva Hoffman avatar Ava HoffmanElizabeth Humphries avatar Elizabeth HumphriesAdelaide Rhodes avatar Adelaide Rhodesorcid logoDave Clements avatar Dave ClementsNatalie Kucher avatar Natalie Kucherorcid logoDaniel Blankenberg avatar Daniel BlankenbergAnton Nekrutenko avatar Anton NekrutenkoMarius van den Beek avatar Marius van den BeekMiguel Roncoroni avatar Miguel RoncoroniFrederick Tan avatar Frederick Tanorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBérénice Batut avatar Bérénice BatutRobert Meller avatar Robert MellerBoris Depoortere avatar Boris DepoortereCandace Savonen avatar Candace SavonenKatherine Cox avatar Katherine CoxSimon Bray avatar Simon Bray

Funders

This material was funded by:

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