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:

Elizabeth Humphries avatar Elizabeth HumphriesMarius van den Beek avatar Marius van den BeekAnton Nekrutenko avatar Anton NekrutenkoRobert Meller avatar Robert Mellerorcid logoBjörn Grüning avatar Björn GrüningNatalie Kucher avatar Natalie Kucherorcid logoHelena Rasche avatar Helena Rascheorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoTeresa Müller avatar Teresa MüllerFrederick Tan avatar Frederick Tanorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSaskia Hiltemann avatar Saskia HiltemannMiguel Roncoroni avatar Miguel RoncoroniJon Trow avatar Jon Troworcid logoDave Clements avatar Dave ClementsAdelaide Rhodes avatar Adelaide Rhodesorcid logoArmin Dadras avatar Armin DadrasAva Hoffman avatar Ava Hoffmanorcid logoBérénice Batut avatar Bérénice BatutCandace Savonen avatar Candace Savonenorcid logoDaniel Blankenberg avatar Daniel BlankenbergMélanie Petera avatar Mélanie PeteraSimon Bray avatar Simon Brayorcid logoMartin Čech avatar Martin ČechBoris Depoortere avatar Boris Depoortereorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBert Droesbeke avatar Bert DroesbekeJasper Ouwerkerk avatar Jasper OuwerkerkKatherine Cox avatar Katherine Cox

Funding

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