{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T06:54:25Z","timestamp":1782024865017,"version":"3.54.5"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252\u2009Gbps in 44.1 and 99.6\u2009h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement.<\/jats:p>\n               <jats:p>Availability and implementation: The source code of MEGAHIT is freely available at https:\/\/github.com\/voutcn\/megahit under GPLv3 license.<\/jats:p>\n               <jats:p>Contact: \u00a0rb@l3-bioinfo.com or twlam@cs.hku.hk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv033","type":"journal-article","created":{"date-parts":[[2015,1,22]],"date-time":"2015-01-22T03:50:58Z","timestamp":1421898658000},"page":"1674-1676","source":"Crossref","is-referenced-by-count":8957,"title":["MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn<\/i> graph"],"prefix":"10.1093","volume":"31","author":[{"given":"Dinghua","family":"Li","sequence":"first","affiliation":[{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi-Man","family":"Liu","sequence":"additional","affiliation":[{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruibang","family":"Luo","sequence":"additional","affiliation":[{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunihiko","family":"Sadakane","sequence":"additional","affiliation":[{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"},{"name":"1 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,1,20]]},"reference":[{"key":"2023020115461644300_btv033-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"2023020115461644300_btv033-B2","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1007\/978-3-642-33122-0_18","article-title":"Succinct de Bruijn Graphs","volume-title":"Algorithms in Bioinformatics","author":"Bowe","year":"2012"},{"key":"2023020115461644300_btv033-B3","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1007\/978-3-642-33122-0_19","article-title":"Space-efficient and exact de Bruijn graph representation based on a bloom filter","volume-title":"Algorithms in Bioinformatics","author":"Chikhi","year":"2012"},{"key":"2023020115461644300_btv033-B4","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020115461644300_btv033-B5","doi-asserted-by":"crossref","first-page":"4904","DOI":"10.1073\/pnas.1402564111","article-title":"Tackling soil diversity with the assembly of large, complex metagenomes","volume":"111","author":"Howe","year":"2014","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020115461644300_btv033-B6","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":"2023020115461644300_btv033-B7","article-title":"GPU-accelerated BWT construction for large collection of short reads","author":"Liu","year":"2014","journal-title":"arXiv"},{"key":"2023020115461644300_btv033-B8","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":"2023020115461644300_btv033-B9","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: a de novo assembler for single-cell and meta-genomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020115461644300_btv033-B10","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/10\/1674\/49013263\/bioinformatics_31_10_1674.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/10\/1674\/49013263\/bioinformatics_31_10_1674.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:14:22Z","timestamp":1675296862000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/10\/1674\/177884"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,20]]},"references-count":10,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2015,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv033","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,5,15]]},"published":{"date-parts":[[2015,1,20]]}}}