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Advances in Bioinformatics
Volume 2015, Article ID 760423, 4 pages
http://dx.doi.org/10.1155/2015/760423
Resource Review

HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis

1Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
2Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA
3Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA

Received 5 September 2015; Accepted 3 December 2015

Academic Editor: David Corne

Copyright © 2015 Ming-an Sun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data. It accepts paired-end hairpin-BS-Seq reads to recover the original (pre-bisulfite-converted) sequences using global alignment and then calls the methylation statuses for cytosines on both DNA strands after mapping the original sequences to the reference genome. After applying to hairpin-BS-Seq datasets, we found that HBS-tools have a reduced mapping time and improved mapping efficiency compared with state-of-the-art mapping tools. The HBS-tools source scripts, along with user guide and testing data, are freely available for download.