Sun, Ming-anVelmurugan, Karthik RajaKeimig, DavidXie, Hehuang David2017-09-182017-09-182015-12-20Ming-an Sun, Karthik Raja Velmurugan, David Keimig, and Hehuang Xie, “HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis,” Advances in Bioinformatics, vol. 2015, Article ID 760423, 4 pages, 2015. doi:10.1155/2015/760423http://hdl.handle.net/10919/78953The 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.application/pdfenCreative Commons Attribution 4.0 InternationalArticle - Refereed2017-09-18Copyright © 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.https://doi.org/10.1155/2015/760423