Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
PLoS One. 2014 Jun 19;9(6):e100360. doi: 10.1371/journal.pone.0100360. eCollection 2014.
DNA methylation, one of the most important epigenetic modifications, plays a crucial role in various biological processes. The level of DNA methylation can be measured using whole-genome bisulfite sequencing at single base resolution. However, until now, there is a paucity of publicly available software for carrying out integrated methylation data analysis. In this study, we implemented Methy-Pipe, which not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data annotation and visualization. Specifically, it uses Burrow-Wheeler Transform (BWT) algorithm to directly align bisulfite sequencing reads to a reference genome and implements a novel sliding window based approach with statistical methods for the identification of differentially methylated regions (DMRs). The capability of processing data parallelly allows it to outperform a number of other bisulfite alignment software packages. To demonstrate its utility and performance, we applied it to both real and simulated bisulfite sequencing datasets. The results indicate that Methy-Pipe can accurately estimate methylation densities, identify DMRs and provide a variety of utility programs for downstream methylation data analysis. In summary, Methy-Pipe is a useful pipeline that can process whole genome bisulfite sequencing data in an efficient, accurate, and user-friendly manner. Software and test dataset are available at http://sunlab.lihs.cuhk.edu.hk/methy-pipe/.
DNA 甲基化是最重要的表观遗传修饰之一，在各种生物过程中起着至关重要的作用。DNA 甲基化的水平可以使用全基因组亚硫酸氢盐测序在单碱基分辨率下进行测量。然而，到目前为止，用于进行综合甲基化数据分析的公开可用软件仍然很少。在这项研究中，我们实现了 Methy-Pipe，它不仅满足了核心数据分析要求（例如序列比对、差异甲基化分析等），还提供了用于甲基化数据注释和可视化的有用工具。具体来说，它使用 Burrow-Wheeler Transform (BWT) 算法将亚硫酸氢盐测序读取直接比对到参考基因组，并实现了一种新颖的基于滑动窗口的方法，结合统计方法来识别差异甲基化区域（DMRs）。其数据并行处理的能力使其优于许多其他亚硫酸氢盐比对软件包。为了证明其效用和性能，我们将其应用于真实和模拟的亚硫酸氢盐测序数据集。结果表明，Methy-Pipe 可以准确估计甲基化密度，识别 DMRs 并为下游甲基化数据分析提供各种实用程序。总之，Methy-Pipe 是一个有用的管道，可以以高效、准确和用户友好的方式处理全基因组亚硫酸氢盐测序数据。软件和测试数据集可在 http://sunlab.lihs.cuhk.edu.hk/methy-pipe/ 获得。
