{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T21:06:25Z","timestamp":1783631185920,"version":"3.55.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":163,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","award":["267591"],"award-info":[{"award-number":["267591"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]},{"name":"ANR Colib\u2019read","award":["ANR-12-BS02-0008"],"award-info":[{"award-number":["ANR-12-BS02-0008"]}]},{"name":"IBC","award":["ANR-11-BINF-0002"],"award-info":[{"award-number":["ANR-11-BINF-0002"]}]},{"name":"D\u00e9fi MASTODONS to E.R., and EU FP7 project SYSCOL","award":["UE7-SYSCOL-258236 to E.U."],"award-info":[{"award-number":["UE7-SYSCOL-258236 to E.U."]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50 000\u2009bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilization of the reads in, e.g. de novo genome assembly. The error correction problem has been tackled either by aligning the long reads against each other or by a hybrid approach that uses the more accurate short reads produced by second generation sequencing technologies to correct the long reads.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present an error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75\u00d7, the throughput of the new method is at least 20% higher.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>LoRMA is freely available at http:\/\/www.cs.helsinki.fi\/u\/lmsalmel\/LoRMA\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw321","type":"journal-article","created":{"date-parts":[[2016,6,7]],"date-time":"2016-06-07T02:23:25Z","timestamp":1465266205000},"page":"799-806","source":"Crossref","is-referenced-by-count":102,"title":["Accurate self-correction of errors in long reads using de Bruijn graphs"],"prefix":"10.1093","volume":"33","author":[{"given":"Leena","family":"Salmela","sequence":"first","affiliation":[{"name":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riku","family":"Walve","sequence":"additional","affiliation":[{"name":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Rivals","sequence":"additional","affiliation":[{"name":"LIRMM and Institut de Biologie Computationelle, CNRS and Universit\u00e9 Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esko","family":"Ukkonen","sequence":"additional","affiliation":[{"name":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,6,6]]},"reference":[{"key":"2023020204511029800_btw321-B1","doi-asserted-by":"crossref","first-page":"e46679","DOI":"10.1371\/journal.pone.0046679","article-title":"Improving PacBio long read accuracy by short read alignment","volume":"7","author":"Au","year":"2012","journal-title":"PLoS ONE"},{"key":"2023020204511029800_btw321-B2","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. 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