Introduction

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/.

Publications

  1. Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.
    Cite this
    Jiang P, Sun K, Lun FM, Guo AM, Wang H, Chan KC, Chiu RW, Lo YM, Sun H, 2014-01-01 - PloS one

Credits

  1. Peiyong Jiang
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  2. Kun Sun
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  3. Fiona M F Lun
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  4. Andy M Guo
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  5. Huating Wang
    Developer

    Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, China

  6. K C Allen Chan
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  7. Rossa W K Chiu
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  8. Y M Dennis Lo
    Developer

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

  9. Hao Sun
    Investigator

    Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, China

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Summary
AccessionBT000036
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl, R
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByHao Sun