{"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":1740185129453,"version":"3.37.3"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2017,6,10]],"date-time":"2017-06-10T00:00:00Z","timestamp":1497052800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,15]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However, their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We present an original and efficient spectral algorithm to layout the uncorrected nanopore reads, and its seamless integration into a straightforward overlap\/layout\/consensus (OLC) assembly scheme. The method is shown to assemble Oxford Nanopore reads from several bacterial genomes into good quality (\u223c99% identity to the reference) genome-sized contigs, while yielding more fragmented assemblies from the eukaryotic microbe Sacharomyces cerevisiae.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n https:\/\/github.com\/antrec\/spectrassembler.<\/jats:p>\n <\/jats:sec>\n \n Supplementary Information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx370","type":"journal-article","created":{"date-parts":[[2017,6,6]],"date-time":"2017-06-06T11:20:12Z","timestamp":1496748012000},"page":"3188-3194","source":"Crossref","is-referenced-by-count":7,"title":["A spectral algorithm for fast de novo<\/i> layout of uncorrected long nanopore reads"],"prefix":"10.1093","volume":"33","author":[{"given":"Antoine","family":"Recanati","sequence":"first","affiliation":[{"name":"CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France"}]},{"given":"Thomas","family":"Br\u00fcls","sequence":"additional","affiliation":[{"name":"Commissariat \u00e0 l\u2019Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Genoscope"},{"name":"UMR 8030, Centre National de la Recherche Scientifique, Universit\u00e9 Paris-Saclay, Evry, France"},{"name":"Universit\u00e9 Paris-Saclay, Evry, France"}]},{"given":"Alexandre","family":"d\u2019Aspremont","sequence":"additional","affiliation":[{"name":"CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2017,6,10]]},"reference":[{"key":"2023020207515093000_btx370-B1","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/S0167-7799(99)01326-8","article-title":"Optical mapping and its potential for large-scale sequencing projects","volume":"17","author":"Aston","year":"1999","journal-title":"Trends in Biotechnology"},{"key":"2023020207515093000_btx370-B2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1137\/S0097539795285771","article-title":"A spectral algorithm for seriation and the consecutive ones problem","volume":"28","author":"Atkins","year":"1998","journal-title":"SIAM Journal on Computing"},{"key":"2023020207515093000_btx370-B3","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S0166-218X(96)00055-8","article-title":"On physical mapping and the consecutive ones property for sparse matrices","volume":"71","author":"Atkins","year":"1996","journal-title":"Discrete Appl. 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