Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites.

ABSTRACT:

Background

Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-lev

SUBMITTER: Furstenau TN 

PROVIDER: S-EPMC5996513 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature