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This article is part of a special issue on epigenomics.

Open Access Highly Accessed Method

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Kasper D Hansen1, Benjamin Langmead12 and Rafael A Irizarry12

Author Affiliations

1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA

2 Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

Genome Biology 2012, 13:R83  doi:10.1186/gb-2012-13-10-r83

Published: 3 October 2012

Abstract

DNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack of comprehensive analytical tools are major challenges that keep this technology from becoming widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software, and can be downloaded from http://rafalab.jhsph.edu/bsmooth webcite.