{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,12,2]],"date-time":"2022-12-02T11:09:46Z","timestamp":1669979386706},"reference-count":14,"publisher":"Hindawi Limited","license":[{"start":{"date-parts":[[2015,12,20]],"date-time":"2015-12-20T00:00:00Z","timestamp":1450569600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"VBI new faculty"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2015,12,20]]},"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.1155\/2015\/760423","type":"journal-article","created":{"date-parts":[[2015,12,20]],"date-time":"2015-12-20T21:01:04Z","timestamp":1450645264000},"page":"1-4","source":"Crossref","is-referenced-by-count":4,"title":["HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis"],"prefix":"10.1155","volume":"2015","author":[{"given":"Ming-an","family":"Sun","sequence":"first","affiliation":[{"name":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Karthik Raja","family":"Velmurugan","sequence":"additional","affiliation":[{"name":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"},{"name":"Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"David","family":"Keimig","sequence":"additional","affiliation":[{"name":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Hehuang","family":"Xie","sequence":"additional","affiliation":[{"name":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"},{"name":"Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA"},{"name":"Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA"}]}],"member":"98","reference":[{"key":"1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl002"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.m411126200"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr017"},{"key":"4","doi-asserted-by":"publisher","DOI":"10.4161\/epi.4.3.8277"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2536758100"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1101\/gr.163147.113"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-232"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-203"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr167"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-10-r82"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq963"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2015\/760423.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2015\/760423.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2015\/760423.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T00:19:13Z","timestamp":1607473153000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2015\/760423\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,20]]},"references-count":14,"alternative-id":["760423","760423"],"URL":"https:\/\/doi.org\/10.1155\/2015\/760423","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"value":"1687-8027","type":"print"},{"value":"1687-8035","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12,20]]}}}