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 Batutorcid logoNicola Soranzo avatar Nicola SoranzoJasper Ouwerkerk avatar Jasper OuwerkerkFrederick Tan avatar Frederick TanBoris Depoortere avatar Boris Depoortereorcid logoTeresa Müller avatar Teresa Müllerorcid logoDave Clements avatar Dave ClementsMiguel Roncoroni avatar Miguel Roncoroniorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn GrüningNatalie Kucher avatar Natalie Kucherorcid logoMartin Čech avatar Martin ČechRobert Meller avatar Robert MellerCandace Savonen avatar Candace Savonenorcid logoWolfgang Maier avatar Wolfgang MaierElizabeth Humphries avatar Elizabeth HumphriesMarius van den Beek avatar Marius van den BeekKatherine Cox avatar Katherine CoxAnton Nekrutenko avatar Anton NekrutenkoAva Hoffman avatar Ava HoffmanSimon Bray avatar Simon Brayorcid logoDaniel Blankenberg avatar Daniel BlankenbergAdelaide Rhodes avatar Adelaide Rhodesorcid logoArmin Dadras avatar Armin Dadrasorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJon Trow avatar Jon TrowMélanie Petera avatar Mélanie Peteraorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano

Funding

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