RRBSMAP：一种快速、准确、用户友好的简化重亚硫酸盐测序比对工具。
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
机构信息
Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
出版信息
Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
SUMMARY
Reduced representation bisulfite sequencing (RRBS) is a powerful yet cost-efficient method for studying DNA methylation on a genomic scale. RRBS involves restriction-enzyme digestion, bisulfite conversion and size selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling RRBS data in a user-friendly and scalable way. RRBSMAP uses wildcard alignment, and avoids the need for any preprocessing or post-processing steps. We benchmarked RRBSMAP against a well-validated MAQ-based pipeline for RRBS read alignment and observed similar accuracy but much improved runtime performance, easier handling and better scaling to large sample sets. In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS.
AVAILABILITY
http://rrbsmap.computational-epigenetics.org/ http://code.google.com/p/bsmap/
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
简化代表性亚硫酸氢盐测序（RRBS）是一种强大且经济高效的方法，可用于在基因组范围内研究 DNA 甲基化。RRBS 涉及限制性内切酶消化、亚硫酸氢盐转化和大小选择，导致需要特殊生物信息学处理的 DNA 测序数据。在这里，我们描述了 RRBSMAP，这是一种短读对齐工具，旨在以用户友好且可扩展的方式处理 RRBS 数据。RRBSMAP 使用通配符对齐，并且不需要任何预处理或后处理步骤。我们将 RRBSMAP 与经过充分验证的基于 MAQ 的 RRBS 读对齐流水线进行了基准测试，观察到相似的准确性，但运行时性能有了很大的提高，处理更加简单，并且可以更好地扩展到大样本集。总之，RRBSMAP 消除了生物信息学障碍，并降低了使用 RRBS 进行大规模表观基因组关联研究的计算负担。
可用性
http://rrbsmap.computational-epigenetics.org/http://code.google.com/p/bsmap/
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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