{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T18:20:34Z","timestamp":1770834034056,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,12,2]],"date-time":"2017-12-02T00:00:00Z","timestamp":1512172800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Bicycle is publicly available under GNU LGPL v3.0 license at http:\/\/www.sing-group.org\/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available.<\/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\/btx778","type":"journal-article","created":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T15:44:20Z","timestamp":1512143060000},"page":"1414-1415","source":"Crossref","is-referenced-by-count":23,"title":["Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data"],"prefix":"10.1093","volume":"34","author":[{"given":"Osvaldo","family":"Gra\u00f1a","sequence":"first","affiliation":[{"name":"Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"},{"name":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S\/N, Universidade de Vigo, Ourense, Spain"}]},{"given":"Hugo","family":"L\u00f3pez-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S\/N, Universidade de Vigo, Ourense, Spain"},{"name":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain"},{"name":"UCIBIO-REQUIMTE, Departamento de Qu\u00edmica, Facultade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, Lisbon, Portugal"}]},{"given":"Florentino","family":"Fdez-Riverola","sequence":"additional","affiliation":[{"name":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S\/N, Universidade de Vigo, Ourense, Spain"},{"name":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain"}]},{"given":"David","family":"Gonz\u00e1lez Pisano","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"given":"Daniel","family":"Glez-Pe\u00f1a","sequence":"additional","affiliation":[{"name":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S\/N, Universidade de Vigo, Ourense, Spain"},{"name":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain"}]}],"member":"286","published-online":{"date-parts":[[2017,12,1]]},"reference":[{"key":"2023012713005766700_btx778-B1","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1093\/bib\/bbu016","article-title":"Methodological aspects of whole-genome bisulfite sequencing analysis","volume":"16","author":"Adusumalli","year":"2015","journal-title":"Brief. Bioinform"},{"key":"2023012713005766700_btx778-B2","doi-asserted-by":"crossref","first-page":"2290","DOI":"10.1093\/hmg\/ddt621","article-title":"Smoke-related DNA methylation changes in the etiology of human disease","volume":"23","author":"Besingi","year":"2014","journal-title":"Hum. Mol. 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