Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.

ABSTRACT: 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 s

SUBMITTER: Jiang P 

PROVIDER: S-EPMC4063866 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature