SONiCS : PCR stutter noise correction in genome-scale microsatellites

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Kedzierska, KZ, Gerber, L, Gacnazzi, D, Krützen, M, Ratan, A & Kistler, L 2018, 'SONiCS : PCR stutter noise correction in genome-scale microsatellites', Bioinformatics.

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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 5 of these markers. In these 110 comparisons, SONiCS showed a 99.1% accuracy rate and a 98.2% genotyping success rate, miscalling a single allele in a marker with low sequence coverage and rejecting another as un-callable.
Availability: Source code and documentation for SONiCS is freely available at https://github.com/kzkedzierska/sonics. Raw read data used in experimental validation of SONiCS have been deposited in the Sequence Read Archive under accession number SRP135756.
Supplementary information: Supplementary data are available at Bioinformatics online.

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