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:

Candace Savonen avatar Candace SavonenKatherine Cox avatar Katherine CoxMarius van den Beek avatar Marius van den Beekorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice BatutNatalie Kucher avatar Natalie Kucherorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton NekrutenkoFrederick Tan avatar Frederick TanBoris Depoortere avatar Boris Depoortereorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoDave Clements avatar Dave ClementsAdelaide Rhodes avatar Adelaide RhodesRobert Meller avatar Robert MellerAva Hoffman avatar Ava HoffmanJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoWolfgang Maier avatar Wolfgang MaierElizabeth Humphries avatar Elizabeth HumphriesMiguel Roncoroni avatar Miguel RoncoroniTeresa Müller avatar Teresa MüllerJon Trow avatar Jon TrowSimon Bray avatar Simon BrayMélanie Petera avatar Mélanie Peteraorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

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