covid19

Tutorials covering covid19

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and 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
covid19 biodiversity

Computational chemistry

Lesson Slides Hands-on Recordings Input dataset Workflows
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
covid19 one-health

Using Galaxy and Managing your Data

Lesson Slides Hands-on Recordings Input dataset Workflows
Automating Galaxy workflows using the command line
workflows variant-analysis covid19
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
ncbi covid19
Submitting sequence data to ENA
covid19

Sequence analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Removal of human reads from SARS-CoV-2 sequencing data
covid19
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1

Variant Analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
covid19 virology one-health
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
covid19 virology one-health

Contributors

This material was contributed to by:

Elizabeth Humphries avatar Elizabeth HumphriesCandace Savonen avatar Candace SavonenMiguel Roncoroni avatar Miguel RoncoroniRobert Meller avatar Robert Mellerorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave Clementsorcid logoBérénice Batut avatar Bérénice Batutorcid logoMarius van den Beek avatar Marius van den Beekorcid logoSaskia Hiltemann avatar Saskia HiltemannMélanie Petera avatar Mélanie Peteraorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoBert Droesbeke avatar Bert DroesbekeKatherine Cox avatar Katherine CoxGildas Le Corguillé avatar Gildas Le Corguilléorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDaniel Blankenberg avatar Daniel BlankenbergFrederick Tan avatar Frederick TanAva Hoffman avatar Ava HoffmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoWolfgang Maier avatar Wolfgang MaierSimon Bray avatar Simon BrayJon Trow avatar Jon TrowBoris Depoortere avatar Boris Depoortereorcid logoArmin Dadras avatar Armin DadrasNatalie Kucher avatar Natalie KucherJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMartin Čech avatar Martin Čechorcid logoBjörn Grüning avatar Björn GrüningAdelaide Rhodes avatar Adelaide Rhodes

Funding

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

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UFR
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NHGRI ANVIL
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BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)
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de.NBI
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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ELIXIR Europe
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NHGRI GDS Community Network
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ELIXIR-CONVERGE
ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement № 871075