An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Abstract 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 accurac...

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Bibliographic Details
Main Authors: Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Goes De Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman, Kristian G. Andersen
Format: Article
Language:English
Published: BMC 2019-01-01
Series:Genome Biology
Subjects:
Viral sequencing
Amplicon sequencing
Intrahost evolution
Zika
West Nile
SNP calling
Online Access:http://link.springer.com/article/10.1186/s13059-018-1618-7

Internet

http://link.springer.com/article/10.1186/s13059-018-1618-7

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