{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T00:13:29Z","timestamp":1722816809167},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements (processing power and memory use) and is optimized to process the upcoming, extended BSseq reads. We optimized the P3BSseq parameters for directional and non-directional libraries, and for single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>P3BSseq binaries and documentation are available at: http:\/\/sourceforge.net\/p\/p3bsseq\/wiki\/Home\/<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw633","type":"journal-article","created":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T19:05:53Z","timestamp":1475262353000},"page":"428-431","source":"Crossref","is-referenced-by-count":13,"title":["P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data"],"prefix":"10.1093","volume":"33","author":[{"given":"Phuc-Loi","family":"Luu","sequence":"first","affiliation":[{"name":"Computational Biology and Bioinformatics, Max Planck Institute for Molecular Biomedicine, M\u00fcnster, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Gerovska","sequence":"additional","affiliation":[{"name":"Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebasti\u00e1n, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikel","family":"Arrospide-Elgarresta","sequence":"additional","affiliation":[{"name":"Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebasti\u00e1n, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sugoi","family":"Retegi-Carri\u00f3n","sequence":"additional","affiliation":[{"name":"Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebasti\u00e1n, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hans R","family":"Sch\u00f6ler","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, M\u00fcnster, Germany"},{"name":"Medical Faculty, University of M\u00fcnster, M\u00fcnster, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos J","family":"Ara\u00fazo-Bravo","sequence":"additional","affiliation":[{"name":"Computational Biology and Bioinformatics, Max Planck Institute for Molecular Biomedicine, M\u00fcnster, Germany"},{"name":"Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebasti\u00e1n, Spain"},{"name":"IKERBASQUE, Basque Foundation for Science, Bilbao, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"key":"2023020204403634700_btw633-B1","doi-asserted-by":"crossref","first-page":"W501","DOI":"10.1093\/nar\/gku457","article-title":"BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives","volume":"42","author":"Becker","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204403634700_btw633-B2","doi-asserted-by":"crossref","first-page":"203.","DOI":"10.1186\/1471-2105-11-203","article-title":"BS Seeker: precise mapping for bisulfite sequencing","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020204403634700_btw633-B3","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1038\/nature09147","article-title":"Relationship between nucleosome positioning and DNA methylation","volume":"466","author":"Chodavarapu","year":"2010","journal-title":"Nature"},{"key":"2023020204403634700_btw633-B4","doi-asserted-by":"crossref","first-page":"485.","DOI":"10.1186\/1471-2105-11-485","article-title":"SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data","volume":"11","author":"Cox","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020204403634700_btw633-B5","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1586\/erm.09.53","article-title":"DNA methylation and cancer diagnosis: new methods and applications","volume":"9","author":"Dehan","year":"2009","journal-title":"Exp. 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