{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:22:49Z","timestamp":1773274969859,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (\u223c30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.<\/jats:p><jats:p>Availability: \u00a0http:\/\/152.2.15.114\/~labweb\/VCAKE<\/jats:p><jats:p>Contact: \u00a0william.jeck@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm451","type":"journal-article","created":{"date-parts":[[2007,9,25]],"date-time":"2007-09-25T00:13:08Z","timestamp":1190679188000},"page":"2942-2944","source":"Crossref","is-referenced-by-count":187,"title":["Extending assembly of short DNA sequences to handle error"],"prefix":"10.1093","volume":"23","author":[{"given":"William R.","family":"Jeck","sequence":"first","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Josephine A.","family":"Reinhardt","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"David A.","family":"Baltrus","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Matthew T.","family":"Hickenbotham","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Vincent","family":"Magrini","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Elaine R.","family":"Mardis","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Jeffery L.","family":"Dangl","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]},{"given":"Corbin D.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Department of Biology, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina\u2014Chapel Hill, Chapel Hill, NC 27599, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,9,24]]},"reference":[{"key":"2023041107264968800_","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","article-title":"Whole-genome re-sequencing","volume":"16","author":"Bentley","year":"2006","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2023041107264968800_","doi-asserted-by":"crossref","first-page":"e484","DOI":"10.1371\/journal.pone.0000484","article-title":"Whole-genome sequencing and assembly with high-throughput, short-read technologies","volume":"2","author":"Sundquist","year":"2007","journal-title":"PLoS ONE"},{"key":"2023041107264968800_","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/btl629","article-title":"Assembling millions of short DNA sequences using SSAKE","volume":"23","author":"Warren","year":"2007","journal-title":"Bioinformatics"},{"key":"2023041107264968800_","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1093\/nar\/gni170","article-title":"An analysis of the feasibility of short read sequencing","volume":"33","author":"Whiteford","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2942\/49822877\/bioinformatics_23_21_2942.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2942\/49822877\/bioinformatics_23_21_2942.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T06:49:02Z","timestamp":1684046942000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/21\/2942\/372853"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,24]]},"references-count":4,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2007,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm451","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,11,1]]},"published":{"date-parts":[[2007,9,24]]}}}