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

J. Gregory Caporaso, 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, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew McKay, Anthony Simard, David M. Engelthaler, Michael Worobey, Paul Keim

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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 genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2's unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.

Original languageEnglish (US)
Article number657
JournalF1000Research
Volume9
DOIs
StatePublished - 2020

Keywords

  • Bioinformatics
  • Genome-sampler
  • Genomics
  • QIIME 2
  • SARS-CoV-2

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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