Lim Jing-Quan, Tennakoon Chandana, Li Guoliang, Wong Eleanor, Ruan Yijun, Wei Chia-Lin, Sung Wing-Kin
Genome Biol. 2012 Oct 3;13(10):R82. doi: 10.1186/gb-2012-13-10-r82.
DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.
DNA甲基化在高等生物中起着至关重要的作用。将亚硫酸氢盐处理与下一代测序相结合，能够对基因组中的5-甲基胞嘧啶位点进行检测。然而，亚硫酸氢盐转化会在测序读数与参考基因组之间引入错配，这使得Illumina和SOLiD读数的映射既缓慢又不准确。BatMeth是一种算法，它集成了新颖的错配计数、列表过滤、错配阶段过滤以及快速映射到两个索引组件，以提高唯一映射率、速度和精度。实验结果表明，BatMeth比现有工具更快、更准确。可从http://code.google.com/p/batmeth/免费获取BatMeth。
