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SONiCS: PCR stutter noise correction in genome-scale microsatellites


Kedzierska, Katarzyna Z; Gerber, Livia; Cagnazzi, Daniele; Krützen, Michael; Ratan, Aakrosh; Kistler, Logan (2018). SONiCS: PCR stutter noise correction in genome-scale microsatellites. Bioinformatics, 34(23):4115-4117.

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 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 and implementation 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.

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 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 and implementation 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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Anthropology
Dewey Decimal Classification:300 Social sciences, sociology & anthropology
Scopus Subject Areas:Physical Sciences > Statistics and Probability
Life Sciences > Biochemistry
Life Sciences > Molecular Biology
Physical Sciences > Computer Science Applications
Physical Sciences > Computational Theory and Mathematics
Physical Sciences > Computational Mathematics
Uncontrolled Keywords:Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications
Language:English
Date:1 December 2018
Deposited On:07 Mar 2019 13:59
Last Modified:15 Apr 2020 23:21
Publisher:Oxford University Press
ISSN:1367-4803
OA Status:Green
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bioinformatics/bty485
Project Information:
  • : FunderSNSF
  • : Grant ID31003A_149956
  • : Project TitleMale career moves - the genomics of cooperative behaviour and alliance formation in male bottlenose dolphins

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