BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

BMC Genomics

Software

Michael Q Zhang¹  Weilong Guo²  Petko Fiziev³  Weihong Yan⁴  Shawn Cokus⁵  Matteo Pellegrini⁶  Pao-Yang Chen⁷  Xueguang Sun⁸ 

[1] Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, 100084, Beijing, China;Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, 75080, Richardson, TX, USA;Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, 100084, Beijing, China;Department of Molecular, Cell and Developmental Biology, University of California, 90095, Los Angeles, CA, USA;Department of Biological Chemistry, University of California, 90095, Los Angeles, CA, USA;Department of Chemistry and Biochemistry, University of California, 90095, Los Angeles, CA, USA;Department of Molecular, Cell and Developmental Biology, University of California, 90095, Los Angeles, CA, USA;Department of Molecular, Cell and Developmental Biology, University of California, 90095, Los Angeles, CA, USA;Institute for Genomics and Proteomics, University of California, 90095, Los Angeles, CA, USA;Institute of Plant and Microbial Biology, Academia Sinica, 11529, Taipei, Taiwan;Zymo Research Corp, 17062 Murphy Ave, 92614, Irvine, CA, USA;

关键词: DNA methylation;    Bisulfite sequencing aligner;    WGBS;    RRBS;    BS Seeker;    Bisulfite conversion failure;    Galaxy toolshed;   

DOI  :  10.1186/1471-2164-14-774

 received in 2013-07-30, accepted in 2013-11-05,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundDNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data.ResultsWe have developed BS-Seeker2, an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes. BS-Seeker2 improves mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy. Moreover, BS-Seeker2 provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing the overestimation of DNA methylation levels. We also defined CGmap and ATCGmap file formats for full representations of DNA methylomes, as part of the outputs of BS-Seeker2 pipeline together with BAM and WIG files.ConclusionsOur evaluations on the performance show that BS-Seeker2 works efficiently and accurately for both WGBS data and RRBS data. BS-Seeker2 is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ and the Galaxy server.

【 授权许可】

Unknown   
© Guo et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.