{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T03:34:06Z","timestamp":1762659246758},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1339,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the estimation of diversity and composition of a sample. To date, there are several tools that aim to remove both sequencing noise and duplicates. Nevertheless, duplicate removal is often based on nucleotide sequences rather than on the underlying flow values, which contain additional information.<\/jats:p>\n               <jats:p>Results: With the novel tool JATAC, we present an approach towards a more accurate duplicate removal by analysing flow values directly. Making use of previous findings on 454 flow data characteristics, we combine read clustering with Bayesian distance measures. Finally, we provide a benchmark with an existing algorithm.<\/jats:p>\n               <jats:p>Availability: JATAC is freely available under the General Public License from http:\/\/malde.org\/ketil\/jatac\/.<\/jats:p>\n               <jats:p>Contact: Ketil.Malde@imr.no<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt047","type":"journal-article","created":{"date-parts":[[2013,2,2]],"date-time":"2013-02-02T02:00:36Z","timestamp":1359770436000},"page":"830-836","source":"Crossref","is-referenced-by-count":17,"title":["Filtering duplicate reads from 454 pyrosequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Susanne","family":"Balzer","sequence":"first","affiliation":[{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"},{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ketil","family":"Malde","sequence":"additional","affiliation":[{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus A.","family":"Grohme","sequence":"additional","affiliation":[{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inge","family":"Jonassen","sequence":"additional","affiliation":[{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"},{"name":"1 Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway, 2Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway, 3Department of Molecular Biotechnology and Functional Genomics, University of Applied Sciences Wildau, Bahnhofstra\u00dfe 1, D-15745 Wildau, Germany and 4Computational Biology Unit, Uni Computing, Thorm\u00f8hlensgate 55, N-5008 Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,2,1]]},"reference":[{"key":"2023020303305408300_btt047-B1","doi-asserted-by":"crossref","first-page":"i420","DOI":"10.1093\/bioinformatics\/btq365","article-title":"Characteristics of 454 pyrosequencing data\u2013enabling realistic simulation with flowsim","volume":"26","author":"Balzer","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020303305408300_btt047-B2","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs","year":"2007","journal-title":"Proc. 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Biophys. Sin. (Shanghai)"},{"key":"2023020303305408300_btt047-B7","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","article-title":"Base-calling of automated sequencer traces using phred. I. Accuracy assessment","volume":"8","author":"Ewing","year":"1998","journal-title":"Genome Res"},{"key":"2023020303305408300_btt047-B8","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II. Error probabilities","volume":"8","author":"Ewing","year":"1998","journal-title":"Genome Res"},{"key":"2023020303305408300_btt047-B9","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2105-11-38","article-title":"SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read","volume":"11","author":"Falgueras","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020303305408300_btt047-B10","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/1471-2164-12-245","article-title":"Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing","volume":"12","author":"Gilles","year":"2011","journal-title":"BMC Genomics"},{"key":"2023020303305408300_btt047-B11","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1038\/ismej.2009.72","article-title":"Systematic artifacts in metagenomes from complex microbial communities","volume":"3","author":"Gomez-Alvarez","year":"2009","journal-title":"ISME J."},{"key":"2023020303305408300_btt047-B12","doi-asserted-by":"crossref","first-page":"e12271","DOI":"10.1371\/journal.pone.0012271","article-title":"Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro","volume":"5","author":"Houseley","year":"2010","journal-title":"PLoS One"},{"key":"2023020303305408300_btt047-B13","doi-asserted-by":"crossref","first-page":"R143","DOI":"10.1186\/gb-2007-8-7-r143","article-title":"Accuracy and quality of massively parallel DNA pyrosequencing","volume":"8","author":"Huse","year":"2007","journal-title":"Genome Biol."},{"key":"2023020303305408300_btt047-B16","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/S1389-1723(03)90130-7","article-title":"Bias and artifacts in multitemplate polymerase chain reactions (PCR)","volume":"96","author":"Kanagawa","year":"2003","journal-title":"J. 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