SARS-CoV-2

Tutorials covering analysis of SARS-CoV-2 (COVID 19)

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Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

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

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoWolfgang Maier avatar Wolfgang Maier

Contributors

This material was contributed to by:

orcid logoTeresa Müller avatar Teresa Müllerorcid logoDaniel Blankenberg avatar Daniel BlankenbergSimon Bray avatar Simon Brayorcid logoBérénice Batut avatar Bérénice Batutorcid logoDave Clements avatar Dave Clementsorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoBoris Depoortere avatar Boris Depoortereorcid logoArmin Dadras avatar Armin Dadrasorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoMartin Čech avatar Martin Čechorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMiguel Roncoroni avatar Miguel RoncoroniCandace Savonen avatar Candace SavonenAva Hoffman avatar Ava HoffmanAdelaide Rhodes avatar Adelaide RhodesFrederick Tan avatar Frederick TanRobert Meller avatar Robert Mellerorcid logoHelena Rasche avatar Helena RascheNatalie Kucher avatar Natalie KucherKatherine Cox avatar Katherine CoxJon Trow avatar Jon TrowMélanie Petera avatar Mélanie PeteraJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoWolfgang Maier avatar Wolfgang MaierMarius van den Beek avatar Marius van den BeekElizabeth Humphries avatar Elizabeth Humphriesorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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