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 logoBérénice Batut avatar Bérénice BatutMélanie Petera avatar Mélanie Peteraorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoHelena Rasche avatar Helena RascheKatherine Cox avatar Katherine Coxorcid logoMartin Čech avatar Martin Čechorcid logoDave Clements avatar Dave ClementsCandace Savonen avatar Candace SavonenJon Trow avatar Jon Troworcid logoAnthony Bretaudeau avatar Anthony BretaudeauJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoArmin Dadras avatar Armin DadrasRobert Meller avatar Robert MellerBoris Depoortere avatar Boris DepoortereNatalie Kucher avatar Natalie Kucherorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMarius van den Beek avatar Marius van den BeekMiguel Roncoroni avatar Miguel Roncoroniorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSaskia Hiltemann avatar Saskia HiltemannFrederick Tan avatar Frederick TanElizabeth Humphries avatar Elizabeth HumphriesSimon Bray avatar Simon BrayAva Hoffman avatar Ava HoffmanAdelaide Rhodes avatar Adelaide RhodesAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüning

Funding

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