{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:02Z","timestamp":1740185102308,"version":"3.37.3"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,5]],"date-time":"2017-05-05T00:00:00Z","timestamp":1493942400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM094146"],"award-info":[{"award-number":["R01GM094146"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000521","name":"Canadian Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000521","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000245","name":"Michael Smith Foundation for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004376","name":"Terry Fox Research Institute","doi-asserted-by":"publisher","award":["TFF-122869"],"award-info":[{"award-number":["TFF-122869"]}],"id":[{"id":"10.13039\/501100004376","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Massively parallel sequencing is now widely used, but data interpretation is only as good as the reference assembly to which it is aligned. While the number of reference assemblies has rapidly expanded, most of these remain at intermediate stages of completion, either as scaffold builds, or as chromosome builds (consisting of correctly ordered, but not necessarily correctly oriented scaffolds separated by gaps). Completion of de novo assemblies remains difficult, as regions that are repetitive or hard to sequence prevent the accumulation of larger scaffolds, and create errors such as misorientations and mislocalizations. Thus, complementary methods for determining the orientation and positioning of fragments are important for finishing assemblies. Strand-seq is a method for determining template strand inheritance in single cells, information that can be used to determine relative genomic distance and orientation between scaffolds, and find errors within them. We present contiBAIT, an R\/Bioconductor package which uses Strand-seq data to repair and improve existing assemblies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>contiBAIT is available on Bioconductor. Source files available from GitHub.<\/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\/btx281","type":"journal-article","created":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T03:10:40Z","timestamp":1493867440000},"page":"2737-2739","source":"Crossref","is-referenced-by-count":11,"title":["Assembling draft genomes using contiBAIT"],"prefix":"10.1093","volume":"33","author":[{"given":"Kieran","family":"O\u2019Neill","sequence":"first","affiliation":[{"name":"Michael Smith Genome Sciences Centre, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada"},{"name":"Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada"}]},{"given":"Mark","family":"Hills","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada"}]},{"given":"Mike","family":"Gottlieb","sequence":"additional","affiliation":[{"name":"Michael Smith Genome Sciences Centre, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada"},{"name":"Bioinformatics Training Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada"}]},{"given":"Matthew","family":"Borkowski","sequence":"additional","affiliation":[{"name":"Independent Researcher, University of British Columbia, Vancouver, BC, Canada"}]},{"given":"Aly","family":"Karsan","sequence":"additional","affiliation":[{"name":"Michael Smith Genome Sciences Centre, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada"},{"name":"Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada"}]},{"given":"Peter M","family":"Lansdorp","sequence":"additional","affiliation":[{"name":"Michael Smith Genome Sciences Centre, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada"},{"name":"Hematology Division, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada"},{"name":"European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2017,5,5]]},"reference":[{"key":"2023020206274435800_btx281-B1","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1038\/nmeth.2206","article-title":"DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution","volume":"9","author":"Falconer","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020206274435800_btx281-B2","doi-asserted-by":"crossref","first-page":"82.","DOI":"10.1186\/gm486","article-title":"BAIT: organizing genomes and mapping rearrangements in single cells","volume":"5","author":"Hills","year":"2013","journal-title":"Genome Med"},{"key":"2023020206274435800_btx281-B3","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023020206274435800_btx281-B4","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1101\/gr.201160.115","article-title":"Characterizing polymorphic inversions in human genomes by single cell sequencing","volume":"26","author":"Sanders","year":"2016","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2737\/49041129\/bioinformatics_33_17_2737.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2737\/49041129\/bioinformatics_33_17_2737.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:29:58Z","timestamp":1675319398000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/17\/2737\/3798628"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,5]]},"references-count":4,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2017,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx281","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,9,1]]},"published":{"date-parts":[[2017,5,5]]}}}