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 Savonenorcid logoBérénice Batut avatar Bérénice BatutJasper Ouwerkerk avatar Jasper OuwerkerkAdelaide Rhodes avatar Adelaide RhodesJon Trow avatar Jon TrowMiguel Roncoroni avatar Miguel RoncoroniBoris Depoortere avatar Boris DepoortereAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena RascheMarius van den Beek avatar Marius van den Beekorcid logoDaniel Blankenberg avatar Daniel BlankenbergAva Hoffman avatar Ava HoffmanMélanie Petera avatar Mélanie PeteraElizabeth Humphries avatar Elizabeth Humphriesorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoTeresa Müller avatar Teresa MüllerRobert Meller avatar Robert Mellerorcid logoWolfgang Maier avatar Wolfgang MaierKatherine Cox avatar Katherine Coxorcid logoSaskia Hiltemann avatar Saskia HiltemannFrederick Tan avatar Frederick TanNatalie Kucher avatar Natalie Kucherorcid logoMartin Čech avatar Martin Čechorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoDave Clements avatar Dave ClementsSimon Bray avatar Simon Brayorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBjörn Grüning avatar Björn Grüningorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoArmin Dadras avatar Armin Dadras

Funding

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