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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

Wolfgang Maier, Simon Bray, View ORCID ProfileMarius van den Beek, Dave Bouvier, Nathaniel Coraor, View ORCID ProfileMilad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P Martin, Andrew Lonie, View ORCID ProfileBjörn Grüning, Sergei L. Kosakovsky Pond, View ORCID ProfileAnton Nekrutenko
doi: https://doi.org/10.1101/2021.03.25.437046
Wolfgang Maier
1, Freiburg, Germany
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Simon Bray
1, Freiburg, Germany
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Marius van den Beek
2, PA, USA
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  • ORCID record for Marius van den Beek
Dave Bouvier
2, PA, USA
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Nathaniel Coraor
2, PA, USA
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Milad Miladi
1, Freiburg, Germany
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Babita Singh
3GalaxyWorks Inc, Baltimore, MD, USA
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Jordi Rambla De Argila
3GalaxyWorks Inc, Baltimore, MD, USA
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Dannon Baker
4Centre for Genomic Regulation, Viral Beacon Project, Barcelona, Spain
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Nathan Roach
5, Baltimore, MD, USA
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Simon Gladman
6, Melbourne, Australia
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Frederik Coppens
7Ghent University, Ghent, Belgium
8VIB Center for Plant Systems Biology, Ghent, Belgium
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Darren P Martin
9University of Cape Town, Cape Town, South Africa
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Andrew Lonie
6, Melbourne, Australia
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Björn Grüning
1, Freiburg, Germany
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  • For correspondence: gruening@informatik.uni-freiburg.de spond@temple.edu aun1@psu.edu
Sergei L. Kosakovsky Pond
10, PA, USA
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  • For correspondence: gruening@informatik.uni-freiburg.de spond@temple.edu aun1@psu.edu
Anton Nekrutenko
2, PA, USA
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  • For correspondence: gruening@informatik.uni-freiburg.de spond@temple.edu aun1@psu.edu
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Abstract

The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.

Competing Interest Statement

Dannon Baker, Nate Coroar, and Anton Nekrutenko are founders of and hold equity in GalaxyWorks, LLC. The results of the study discussed in this publication could affect the value of GalaxyWorks, LLC.

Footnotes

  • https://covid19.galaxyproject.org

  • https://usegalaxy.org

  • https://usegalaxy.eu

  • https://usegalaxy.org.au

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathaniel Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P Martin, Andrew Lonie, Björn Grüning, Sergei L. Kosakovsky Pond, Anton Nekrutenko
bioRxiv 2021.03.25.437046; doi: https://doi.org/10.1101/2021.03.25.437046
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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathaniel Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P Martin, Andrew Lonie, Björn Grüning, Sergei L. Kosakovsky Pond, Anton Nekrutenko
bioRxiv 2021.03.25.437046; doi: https://doi.org/10.1101/2021.03.25.437046

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