{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:29Z","timestamp":1740185129746,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,13]],"date-time":"2017-10-13T00:00:00Z","timestamp":1507852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>De novo genome assembly of next-generation sequencing data is a fundamental problem in bioinformatics. There are many programs that assemble small genomes, but very few can assemble whole human genomes. We present a new algorithm for parallel overlap graph construction, which is capable of assembling human genomes and improves upon the current state-of-the-art in genome assembly.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SAGE2 is written in C\u2009++\u2009and OpenMP and is freely available (under the GPL 3.0 license) at github.com\/lucian-ilie\/SAGE2.<\/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\/btx648","type":"journal-article","created":{"date-parts":[[2017,10,12]],"date-time":"2017-10-12T19:30:19Z","timestamp":1507836619000},"page":"678-680","source":"Crossref","is-referenced-by-count":2,"title":["SAGE2: parallel human genome assembly"],"prefix":"10.1093","volume":"34","author":[{"given":"Michael","family":"Molnar","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, ON, Canada"}]},{"given":"Ehsan","family":"Haghshenas","sequence":"additional","affiliation":[{"name":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada"}]},{"given":"Lucian","family":"Ilie","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, ON, Canada"}]}],"member":"286","published-online":{"date-parts":[[2017,10,13]]},"reference":[{"key":"2023012712394102200_btx648-B1","doi-asserted-by":"crossref","first-page":"302.","DOI":"10.1186\/1471-2105-15-302","article-title":"SAGE: string-overlap assembly of genomes","volume":"15","author":"Ilie","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023012712394102200_btx648-B2","doi-asserted-by":"crossref","first-page":"709.","DOI":"10.1186\/s13104-015-1682-y","article-title":"LASER: Large genome ASsembly EvaluatoR","volume":"8","author":"Khiste","year":"2015","journal-title":"BMC Res. Notes"},{"key":"2023012712394102200_btx648-B3","doi-asserted-by":"crossref","first-page":"18.","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"key":"2023012712394102200_btx648-B4","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","article-title":"Efficient de novo assembly of large genomes using compressed data structures","volume":"22","author":"Simpson","year":"2012","journal-title":"Genome Res"},{"key":"2023012712394102200_btx648-B5","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res"},{"key":"2023012712394102200_btx648-B6","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1038\/ng.3121","article-title":"Comprehensive variation discovery in single human genomes","volume":"46","author":"Weisenfeld","year":"2014","journal-title":"Nat. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/678\/48914396\/bioinformatics_34_4_678.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/678\/48914396\/bioinformatics_34_4_678.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:41:21Z","timestamp":1674823281000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/4\/678\/4553153"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,10,13]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2018,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx648","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,2,15]]},"published":{"date-parts":[[2017,10,13]]}}}