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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Maier, Wolfgang Bray, Simon van den Beek, Marius Bouvier, Dave Coraor, Nathaniel Miladi, Milad Singh, Babita Rambla De Argila, Jordi Baker, Dannon Roach, Nathan
Maier, Wolfgang
Bray, Simon
van den Beek, Marius
Bouvier, Dave
Coraor, Nathaniel
Miladi, Milad
Singh, Babita
Rambla De Argila, Jordi
Baker, Dannon
Roach, Nathan
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Pre-print
Date
2021-03-25
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Biology
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https://doi.org/10.1101/2021.03.25.437046
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.
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