{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T11:52:30Z","timestamp":1775908350287,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T00:00:00Z","timestamp":1605830400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-2014-CoG"],"award-info":[{"award-number":["ERC-2014-CoG"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["648143"],"award-info":[{"award-number":["648143"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Linked genomic sequencing reads contain information that can be used to join sequences together into scaffolds in draft genome assemblies. Existing software for this purpose performs the scaffolding by joining sequences with a gap between them, not considering potential overlaps of contigs. We developed ARBitR to create scaffolds where overlaps are taken into account and show that it can accurately recreate regions where draft assemblies are broken.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ARBitR is written and implemented in Python3 for Unix-based operative systems. All source code is available at https:\/\/github.com\/markhilt\/ARBitR under the GNU General Public License v3.<\/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\/btaa975","type":"journal-article","created":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T20:56:59Z","timestamp":1605041819000},"page":"2203-2205","source":"Crossref","is-referenced-by-count":21,"title":["ARBitR: an overlap-aware genome assembly scaffolder for linked reads"],"prefix":"10.1093","volume":"37","author":[{"given":"Markus","family":"Hiltunen","sequence":"first","affiliation":[{"name":"Department of Organismal Biology, Uppsala University , 75236 Uppsala, Sweden"}]},{"given":"Martin","family":"Ryberg","sequence":"additional","affiliation":[{"name":"Department of Organismal Biology, Uppsala University , 75236 Uppsala, Sweden"}]},{"given":"Hanna","family":"Johannesson","sequence":"additional","affiliation":[{"name":"Department of Organismal Biology, Uppsala University , 75236 Uppsala, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2020,11,20]]},"reference":[{"key":"2023061310311764400_btaa975-B1","doi-asserted-by":"crossref","first-page":"1570","DOI":"10.1101\/gr.191189.115","article-title":"Read clouds uncover variation in complex regions of the human genome","volume":"25","author":"Bishara","year":"2015","journal-title":"Genome Res"},{"key":"2023061310311764400_btaa975-B2","doi-asserted-by":"crossref","first-page":"R56","DOI":"10.1186\/gb-2012-13-6-r56","article-title":"Toward almost closed genomes with GapFiller","volume":"13","author":"Boetzer","year":"2012","journal-title":"Genome Biol"},{"key":"2023061310311764400_btaa975-B3","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1186\/s12859-018-2243-x","article-title":"ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers","volume":"19","author":"Coombe","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023061310311764400_btaa975-B4","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/nbt0515-433","article-title":"Startups use short-read data to expand long-read sequencing market","volume":"33","author":"Eisenstein","year":"2015","journal-title":"Nat. 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