{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,11]],"date-time":"2024-05-11T05:59:22Z","timestamp":1715407162724},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Paired-end sequencing resulting in gapped short reads is commonly used for de novo genome assembly. Assembly methods use paired-end sequences in a two-step process, first treating each read-end independently, only later invoking the pairing to join the contiguous assemblies (contigs) into gapped scaffolds. Here, we present ELOPER, a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.<\/jats:p>\n               <jats:p>Results: ELOPER proceeds by simultaneously considering both ends of paired reads generating elongated reads. We show that ELOPER theoretically doubles read-lengths while halving the number of reads. We provide evidence that pre-processing read libraries using ELOPER leads to considerably improved assemblies as predicted from the Lander\u2013Waterman model.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/sourceforge.net\/projects\/eloper.<\/jats:p>\n               <jats:p>Contact: \u00a0yanai@technion.ac.il<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt169","type":"journal-article","created":{"date-parts":[[2013,4,20]],"date-time":"2013-04-20T02:09:34Z","timestamp":1366423774000},"page":"1455-1457","source":"Crossref","is-referenced-by-count":7,"title":["ELOPER: elongation of paired-end reads as a pre-processing tool for improved <i>de novo<\/i> genome assembly"],"prefix":"10.1093","volume":"29","author":[{"given":"David H.","family":"Silver","sequence":"first","affiliation":[{"name":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shay","family":"Ben-Elazar","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexei","family":"Bogoslavsky","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Itai","family":"Yanai","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,4,19]]},"reference":[{"key":"2023062610153360300_btt169-B1","first-page":"177","article-title":"ARACHNE: a whole-genome shotgun assembler","volume":"12","author":"Batzoglou","year":"2002","journal-title":"Genome Res."},{"key":"2023062610153360300_btt169-B2","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","article-title":"Genomic mapping by fingerprinting random clones: a mathematical analysis","volume":"2","author":"Lander","year":"1988","journal-title":"Genomics"},{"key":"2023062610153360300_btt169-B3","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1101\/gr.097261.109","article-title":"De novo assembly of human genomes with massively parallel short read sequencing","volume":"20","author":"Li","year":"2010","journal-title":"Genome Res."},{"key":"2023062610153360300_btt169-B4","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.ygeno.2010.03.001","article-title":"Assembly algorithms for next-generation sequencing data","volume":"95","author":"Miller","year":"2010","journal-title":"Genomics"},{"key":"2023062610153360300_btt169-B5","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1073\/pnas.1115467109","article-title":"A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans","volume":"109","author":"Sabehi","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/11\/1455\/50700999\/bioinformatics_29_11_1455.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/11\/1455\/50700999\/bioinformatics_29_11_1455.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T10:16:12Z","timestamp":1687774572000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/11\/1455\/220785"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,19]]},"references-count":5,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt169","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,6,1]]},"published":{"date-parts":[[2013,4,19]]}}}