{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T10:46:14Z","timestamp":1781001974693,"version":"3.54.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation : Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega ( o verlap-graph me ta g enome a ssembler) was developed for assembling and scaffolding Illumina sequencing data of microbial communities.<\/jats:p><jats:p>Results : Omega found overlaps between reads using a prefix\/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information. In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.<\/jats:p><jats:p>Availability and implementation : Implemented in C++ with source code and binaries freely available at http:\/\/omega.omicsbio.org .<\/jats:p><jats:p>Contact : panc@ornl.gov<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu395","type":"journal-article","created":{"date-parts":[[2014,6,20]],"date-time":"2014-06-20T06:59:59Z","timestamp":1403247599000},"page":"2717-2722","source":"Crossref","is-referenced-by-count":88,"title":["Omega: an Overlap-graph<i>de novo<\/i>Assembler for Metagenomics"],"prefix":"10.1093","volume":"30","author":[{"given":"Bahlul","family":"Haider","sequence":"first","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tae-Hyuk","family":"Ahn","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Bushnell","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juanjuan","family":"Chai","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Copeland","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chongle","family":"Pan","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and 2 U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,6,19]]},"reference":[{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1101\/gr.7337908","article-title":"ALLPATHS: de novo assembly of whole-genome shotgun microreads","volume":"18","author":"Butler","year":"2008","journal-title":"Genome Res."},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jagm.1995.0805","article-title":"An efficient implementation of a scaling minimum-cost flow algorithm","volume":"22","author":"Goldberg","year":"1997","journal-title":"J. Algorithms"},{"key":"2023041303355933300_","volume-title":"A New Algorithm for De Novo Genome Assembly","author":"Haider","year":"2012"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1093\/bioinformatics\/btr520","article-title":"Bambus 2: scaffolding metagenomes","volume":"27","author":"Koren","year":"2011","journal-title":"Bioinformatics"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041303355933300_","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":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","article-title":"A whole-genome assembly of Drosophila","volume":"287","author":"Myers","year":"2000","journal-title":"Science"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"ii79","DOI":"10.1093\/bioinformatics\/bti1114","article-title":"The fragment assembly string graph","volume":"21","author":"Myers","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1093\/nar\/gks678","article-title":"MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads","volume":"40","author":"Namiki","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1007\/978-3-642-12683-3_28","article-title":"IDBA\u2014A Practical Iterative de Bruijn Graph De Novo Assembler","volume-title":"Research in Computational Molecular Biology","author":"Peng","year":"2010"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2012","journal-title":"Bioinformatics"},{"key":"2023041303355933300_","author":"Pop","year":"2011"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"e3373","DOI":"10.1371\/journal.pone.0003373","article-title":"MetaSim: a sequencing simulator for genomics and metagenomics","volume":"3","author":"Richter","year":"2008","journal-title":"PloS One"},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1111\/1462-2920.12086","article-title":"Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities","volume":"15","author":"Shakya","year":"2013","journal-title":"Environ. Microbiol."},{"key":"2023041303355933300_","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":"2023041303355933300_","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":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"R2","DOI":"10.1186\/gb-2013-14-1-r2","article-title":"MetAMOS: a modular and open source metagenomic assembly and analysis pipeline","volume":"14","author":"Treangen","year":"2013","journal-title":"Genome Biol."},{"key":"2023041303355933300_","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/19\/2717\/49872352\/bioinformatics_30_19_2717.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/19\/2717\/49872352\/bioinformatics_30_19_2717.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T12:35:01Z","timestamp":1689338101000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/19\/2717\/2422265"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,19]]},"references-count":19,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2014,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu395","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,10]]},"published":{"date-parts":[[2014,6,19]]}}}