{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T09:43:30Z","timestamp":1781775810306,"version":"3.54.5"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T00:00:00Z","timestamp":1508716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG007182"],"award-info":[{"award-number":["R01HG007182"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000233","name":"Genome British Columbia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000233","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA\u2014a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10\u2009\u00d7\u2009Genomics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/bcgsc\/ARCS\/<\/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\/btx675","type":"journal-article","created":{"date-parts":[[2017,10,20]],"date-time":"2017-10-20T15:13:35Z","timestamp":1508512415000},"page":"725-731","source":"Crossref","is-referenced-by-count":190,"title":["ARCS: scaffolding genome drafts with linked reads"],"prefix":"10.1093","volume":"34","author":[{"given":"Sarah","family":"Yeo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Coombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9890-2293","authenticated-orcid":false,"given":"Ren\u00e9 L","family":"Warren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0950-7839","authenticated-orcid":false,"given":"Inan\u00e7","family":"Birol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"2023012712405439900_btx675-B1","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1101\/gr.178319.114","article-title":"In vitro, long-range sequence information for de novo genome assembly via transposase contiguity","volume":"24","author":"Adey","year":"2014","journal-title":"Genome Res"},{"key":"2023012712405439900_btx675-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023012712405439900_btx675-B3","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023012712405439900_btx675-B4","doi-asserted-by":"crossref","first-page":"R42.","DOI":"10.1186\/gb-2014-15-3-r42","article-title":"A comprehensive evaluation of assembly scaffolding tools","volume":"15","author":"Hunt","year":"2014","journal-title":"Genome Biol"},{"key":"2023012712405439900_btx675-B5","doi-asserted-by":"crossref","DOI":"10.1101\/gr.214346.116","article-title":"ABySS 2.0: resource-efficient assembly of large genomes using a bloom filter","author":"Jackman","year":"2017","journal-title":"Genome Res"},{"key":"2023012712405439900_btx675-B6","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/nbt.2833","article-title":"Whole-genome haplotyping using long reads and statistical methods","volume":"32","author":"Kuleshov","year":"2014","journal-title":"Nat. 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