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:

Jasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoNicola Soranzo avatar Nicola SoranzoMarius van den Beek avatar Marius van den BeekBoris Depoortere avatar Boris Depoortereorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoJon Trow avatar Jon Troworcid logoSaskia Hiltemann avatar Saskia HiltemannMélanie Petera avatar Mélanie Peteraorcid logoTeresa Müller avatar Teresa Müllerorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoHelena Rasche avatar Helena Rascheorcid logoArmin Dadras avatar Armin Dadrasorcid logoAnthony Bretaudeau avatar Anthony BretaudeauKatherine Cox avatar Katherine Coxorcid logoDave Clements avatar Dave ClementsNatalie Kucher avatar Natalie Kucherorcid logoDaniel Blankenberg avatar Daniel BlankenbergAnton Nekrutenko avatar Anton NekrutenkoCandace Savonen avatar Candace Savonenorcid logoBjörn Grüning avatar Björn GrüningElizabeth Humphries avatar Elizabeth HumphriesSimon Bray avatar Simon BrayAva Hoffman avatar Ava Hoffmanorcid logoBérénice Batut avatar Bérénice BatutRobert Meller avatar Robert Mellerorcid logoMartin Čech avatar Martin ČechFrederick Tan avatar Frederick TanAdelaide Rhodes avatar Adelaide Rhodesorcid logoWolfgang Maier avatar Wolfgang MaierMiguel Roncoroni avatar Miguel Roncoroni

Funding

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