{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T10:06:02Z","timestamp":1774519562367,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,21]],"date-time":"2018-08-21T00:00:00Z","timestamp":1534809600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"FP7-HEALTH: READNA"},{"DOI":"10.13039\/100011260","name":"FP7-INFRASTRUCTURES","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011260","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ESGI"},{"name":"BLUEPRINT"},{"name":"Spanish Ministry of Economy, Industry and Competitiveness","award":["BIO2015"],"award-info":[{"award-number":["BIO2015"]}]},{"name":"Spanish Ministry of Economy, Industry and Competitiveness","award":["71969 REDI"],"award-info":[{"award-number":["71969 REDI"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools are becoming rapidly outdated as they lack sensible functionality and efficiency to handle large amounts of data now commonly created.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed gemBS, a fast high-throughput bioinformatics pipeline specifically designed for large scale BS-Seq analysis that combines a high performance BS-mapper (GEM3) and a variant caller specifically for BS-Seq data (BScall). gemBS provides genotype information and methylation estimates for all genomic cytosines in different contexts (CpG and non-CpG) and a set of quality reports for comprehensive and reproducible analysis. gemBS is highly modular and can be easily automated, while producing robust and accurate results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>gemBS is released under the GNU GPLv3+ license. Source code and documentation are freely available from www.statgen.cat\/gemBS.<\/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\/bty690","type":"journal-article","created":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T07:34:30Z","timestamp":1534750470000},"page":"737-742","source":"Crossref","is-referenced-by-count":59,"title":["gemBS: high throughput processing for DNA methylation data from bisulfite sequencing"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5164-6803","authenticated-orcid":false,"given":"Angelika","family":"Merkel","sequence":"first","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG-CRG), Centre de Regulacio Gen\u00f3mico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos","family":"Fern\u00e1ndez-Callejo","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG-CRG), Centre de Regulacio Gen\u00f3mico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eloi","family":"Casals","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG-CRG), Centre de Regulacio Gen\u00f3mico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santiago","family":"Marco-Sola","sequence":"additional","affiliation":[{"name":"Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronald","family":"Schuyler","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivo G","family":"Gut","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG-CRG), Centre de Regulacio Gen\u00f3mico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon C","family":"Heath","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG-CRG), Centre de Regulacio Gen\u00f3mico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,21]]},"reference":[{"key":"2023013107260099500_bty690-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.12688\/f1000research.2-217.v1","article-title":"MethylExtract: high-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data","volume":"2","author":"Barturen","year":"2013","journal-title":"F1000Research"},{"key":"2023013107260099500_bty690-B2","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/nrg3273","article-title":"Analysing and interpreting DNA methylation data","volume":"13","author":"Bock","year":"2012","journal-title":"Nat. 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