SONiCS：全基因组微卫星中的 PCR 重迭噪音校正。
SONiCS: PCR stutter noise correction in genome-scale microsatellites.
机构信息
Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
Evolutionary Genetics Group, Department of Anthropology, University of Zurich, CH-8057 Zurich, Switzerland.
出版信息
Bioinformatics. 2018 Dec 1;34(23):4115-4117. doi: 10.1093/bioinformatics/bty485.
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.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
大量平行捕获短串联重复序列（STR，或微卫星）为种群基因组学和人口统计学分析提供了一种策略，可以在有或没有参考基因组的情况下进行高分辨率分析。然而，目标捕获实验所需的高聚合酶链反应（PCR）循环数会通过聚合酶滑动产生称为 PCR 重影的基因分型噪声。
结果
我们开发了 SONiCS-Stutter mONte Carlo Simulation，这是一种基于 PCR 和捕获实验条件的密集正向模拟的重影校正解决方案。为了测试 SONiCS，我们使用目标捕获对 22 头弓头鲸（ Sousa sahulensis ）进行了 2499 个标记 STR 面板的基因分型，并生成了毛细管基基因分型来验证其中的 5 个标记。在这 110 次比较中，SONiCS 的准确率为 99.1%，基因分型成功率为 98.2%，在一个序列覆盖率低的标记中误报了一个等位基因，并拒绝了另一个标记无法进行基因分型。
可用性和实现
SONiCS 的源代码和文档可在 https://github.com/kzkedzierska/sonics 上免费获得。用于 SONiCS 实验验证的原始读取数据已在序列读取档案中以 accession number SRP135756 形式存储。
补充信息
补充数据可在生物信息学在线获得。
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