{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T09:14:42Z","timestamp":1777108482365,"version":"3.51.4"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing technologies produce large sets of short reads that may contain errors. These sequencing errors make de novo assembly challenging. Error correction aims to reduce the error rate prior assembly. Many de novo sequencing projects use reads from several sequencing technologies to get the benefits of all used technologies and to alleviate their shortcomings. However, combining such a mixed set of reads is problematic as many tools are specific to one sequencing platform. The SOLiD sequencing platform is especially problematic in this regard because of the two base color coding of the reads. Therefore, new tools for working with mixed read sets are needed.<\/jats:p>\n               <jats:p>Results: We present an error correction tool for correcting substitutions, insertions and deletions in a mixed set of reads produced by various sequencing platforms. We first develop a method for correcting reads from any sequencing technology producing base space reads such as the SOLEXA\/Illumina and Roche\/454 Life Sciences sequencing platforms. We then further refine the algorithm to correct the color space reads from the Applied Biosystems SOLiD sequencing platform together with normal base space reads. Our new tool is based on the SHREC program that is aimed at correcting SOLEXA\/Illumina reads. Our experiments show that we can detect errors with 99% sensitivity and &amp;gt;98% specificity if the combined sequencing coverage of the sets is at least 12. We also show that the error rate of the reads is greatly reduced.<\/jats:p>\n               <jats:p>Availability: The JAVA source code is freely available at http:\/\/www.cs.helsinki.fi\/u\/lmsalmel\/hybrid-shrec\/<\/jats:p>\n               <jats:p>Contact: \u00a0leena.salmela@cs.helsinki.fi<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq151","type":"journal-article","created":{"date-parts":[[2010,4,9]],"date-time":"2010-04-09T00:19:08Z","timestamp":1270772348000},"page":"1284-1290","source":"Crossref","is-referenced-by-count":77,"title":["Correction of sequencing errors in a mixed set of reads"],"prefix":"10.1093","volume":"26","author":[{"given":"Leena","family":"Salmela","sequence":"first","affiliation":[{"name":"Department of Computer Science, PO Box 68 (Gustaf H\u00e4llstr\u00f6min katu 2b), FI-00014 University of Helsinki, Finland"}]}],"member":"286","published-online":{"date-parts":[[2010,4,8]]},"reference":[{"key":"2023012507513086100_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023012507513086100_B2","author":"Applied Biosystems Incorporated","year":"2008","journal-title":"Principles of di-base sequencing and the advantages of color space analysis in the SOLiD system."},{"key":"2023012507513086100_B3","author":"Applied Biosystems Incorporated","year":"2008","journal-title":"A theoretical understanding of 2 base color codes and its application to annotation, error detection, and error correction."},{"key":"2023012507513086100_B4","first-page":"177","article-title":"ARACHNE: a whole-genome shotgun assembler","volume":"12","author":"Batzoglou","year":"2002","journal-title":"Genome Res."},{"key":"2023012507513086100_B5","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":"2023012507513086100_B6","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1093\/bioinformatics\/bth205","article-title":"Fragment assembly with short reads","volume":"20","author":"Chaisson","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507513086100_B7","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","article-title":"SOAP2: an improved ultrafast tool for short read alignment","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507513086100_B8","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":"2023012507513086100_B9","doi-asserted-by":"crossref","first-page":"9748","DOI":"10.1073\/pnas.171285098","article-title":"An Eulerian path approach to DNA fragment assembly","volume":"98","author":"Pevzner","year":"2001","journal-title":"Proc. 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Biotechnol."},{"key":"2023012507513086100_B13","doi-asserted-by":"crossref","first-page":"4662","DOI":"10.1093\/nar\/gkg653;","article-title":"Correcting errors in shotgun sequences","volume":"31","author":"Tammi","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012507513086100_B14","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\/26\/10\/1284\/48851226\/bioinformatics_26_10_1284.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/10\/1284\/48851226\/bioinformatics_26_10_1284.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:51:42Z","timestamp":1674633102000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/10\/1284\/194027"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,8]]},"references-count":14,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2010,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq151","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,5,15]]},"published":{"date-parts":[[2010,4,8]]}}}