SONiCS: PCR stutter noise correction in genome-scale microsatellites.

ABSTRACT:

Motivation

Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through polymerase slippage known as PCR stutter.

Results

We developed SONiCS-Stutter mONte Carlo Simulation-a solution for stutter correction based on dense forward simulations of PCR and capture experimental conditions. To test SONiCS, we genotyped a 2499-marker STR panel in 22 humpback dolphins (Sousa sahulensis) using target capture, and generated capillary-based genotypes to validate five of these markers. In these 110 comparisons, SONiCS

SUBMITTER: Kedzierska KZ 

PROVIDER: S-EPMC6454461 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature