Article
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Genome biology - 8 Jan 2019
Grubaugh Nathan D, Gangavarapu Karthik, Quick Joshua, Matteson Nathaniel L, De Jesus Jaqueline Goes, Main Bradley J, Tan Amanda L, Paul Lauren M, Brackney Doug E, Grewal Saran, Gurfield Nikos, Van Rompay Koen K A, Isern Sharon, Michael Scott F, Coffey Lark L, Loman Nicholas J, Andersen Kristian G
Abstract excerpt
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using...
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