Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

Evan Bolyen; Matthew R. Dillon; Nicholas A. Bokulich; Jason T. Ladner; Brendan B. Larsen; Crystal M. Hepp; Darrin Lemmer; Jason W. Sahl; Andrew Sanchez; Chris Holdgraf; Paul Keim; J. Gregory Caporaso

doi:https://doi.org/10.12688/f1000research.24751.2

doi.org/10.12688/f1000research.24751.2

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

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..., J. Gregory Caporaso

64

F1000Research

Volume: 9, Pages: 657 - 657

Published: Oct 28, 2020

Abstract

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of...

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Paper Details

Title

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

DOI

doi.org/10.12688/f1000research.24751.2

Published Date

Oct 28, 2020

Journal

F1000Research

Volume

9

Pages

657 - 657

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