BS-SNPer：亚硫酸氢盐测序数据中的单核苷酸多态性（SNP）检测
BS-SNPer: SNP calling in bisulfite-seq data.
作者信息
Gao Shengjie, Zou Dan, Mao Likai, Liu Huayu, Song Pengfei, Chen Youguo, Zhao Shancen, Gao Changduo, Li Xiangchun, Gao Zhibo, Fang Xiaodong, Yang Huanming, Ørntoft Torben F, Sørensen Karina D, Bolund Lars
机构信息
Department of Biomedicine, Aarhus University, Aarhus, Denmark, BGI Co. Ltd., Shenzhen 518083, China, BioInformatics Research Center (BIRC), Aarhus University, Aarhus 8000, Denmark.
BGI Co. Ltd., Shenzhen 518083, China, School of Computer, National University of Defense Technology, Changsha 410073, China.
出版信息
Bioinformatics. 2015 Dec 15;31(24):4006-8. doi: 10.1093/bioinformatics/btv507. Epub 2015 Aug 28.
UNLABELLED
Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here, we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared with Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared with existing methods.
AVAILABILITY AND IMPLEMENTATION
BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.
未加标签
亚硫酸氢钠转化后测序（BS-Seq，如全基因组亚硫酸氢盐测序或简化代表性亚硫酸氢盐测序）已成为研究人类表观遗传图谱的常用方法。识别单核苷酸多态性（SNP）对于甲基化水平的定量以及诸如印记等等位基因特异性表观遗传事件的研究非常重要。然而，在此类数据中进行SNP检测既复杂又耗时。在此，我们提出了一个名为BS-SNPer的超快速且内存高效的软件包，用于从BS-Seq数据中探索SNP位点。与流行的BS-Seq特异性SNP检测工具Bis-SNP相比，BS-SNPer的速度快100多倍，且内存使用更少。与现有方法相比，BS-SNPer还具有更高的灵敏度和特异性。
可用性和实现方式
BS-SNPer用C++和Perl编写，可在https://github.com/hellbelly/BS-Snper上免费获取。
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