{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T09:03:53Z","timestamp":1778144633753,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T00:00:00Z","timestamp":1567123200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Research Council Advanced grant to PML"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we introduce breakpointR, an R\/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R\/Bioconductor package https:\/\/bioconductor.org\/packages\/breakpointR.<\/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\/btz681","type":"journal-article","created":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T18:46:49Z","timestamp":1567018009000},"page":"1260-1261","source":"Crossref","is-referenced-by-count":45,"title":["breakpointR: an R\/Bioconductor package to localize strand state changes in Strand-seq data"],"prefix":"10.1093","volume":"36","author":[{"given":"David","family":"Porubsky","sequence":"first","affiliation":[{"name":"European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands"},{"name":"Department of Genome Sciences, University of Washington School of Medicine , Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashley D","family":"Sanders","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, BC Cancer Agency , Vancouver, BC, Canada"},{"name":"European Molecular Biology Laboratory (EMBL), Genome Biology Unit , Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9639-2306","authenticated-orcid":false,"given":"Aaron","family":"Taudt","sequence":"additional","affiliation":[{"name":"European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands"},{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen , Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Colom\u00e9-Tatch\u00e9","sequence":"additional","affiliation":[{"name":"European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands"},{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen , Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter M","family":"Lansdorp","sequence":"additional","affiliation":[{"name":"European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands"},{"name":"Terry Fox Laboratory, BC Cancer Agency , Vancouver, BC, Canada"},{"name":"Department of Medical Genetics, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"Guryev","sequence":"additional","affiliation":[{"name":"European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,30]]},"reference":[{"key":"2023013110150810800_btz681-B1","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/nprot.2012.039","article-title":"Genome-wide copy number analysis of single cells","volume":"7","author":"Baslan","year":"2012","journal-title":"Nat. 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