sap—a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery使整个序列映射和分析程序长时间序列读取校准和准确的变异的发现.pdfVIP

SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery Zheng Sun, Weidong Tian* State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China Abstract The third-generation of sequencing technologies produces sequence reads of 1000 bp or more that may contain high polymorphism information. However, most currently available sequence analysis tools are developed specifically for analyzing short sequence reads. While the traditional Smith-Waterman (SW) algorithm can be used to map long sequence reads, its naive implementation is computationally infeasible. We have developed a new Sequence mapping and Analyzing Program (SAP) that implements a modified version of SW to speed up the alignment process. In benchmarks with simulated and real exon sequencing data and a real E. coli genome sequence data generated by the third-generation sequencing technologies, SAP outperforms currently available tools for mapping short and long sequence reads in both speed and proportion of captured reads. In addition, it achieves high accuracy in detecting SNPs and InDels in the simulated data. SAP is available at /davidsun/SAP. Citation: Sun Z, Tian W (2012) SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery. PLoS ONE 7(8): e42887. doi:10.1371/journal.pone.0042887 Editor: Haixu Tang, Indiana University, United States of America Received April 16, 2012; Accepted July 12, 2012; Published August 7, 2012 Copyright: 2012 Sun, Tian. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and sourc