{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T11:19:52Z","timestamp":1774783192410,"version":"3.50.1"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,3,15]],"date-time":"2015-03-15T00:00:00Z","timestamp":1426377600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0520-5","type":"journal-article","created":{"date-parts":[[2015,3,14]],"date-time":"2015-03-14T10:46:30Z","timestamp":1426329990000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads"],"prefix":"10.1186","volume":"16","author":[{"given":"Mohamed","family":"Mysara","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie","family":"Leys","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeroen","family":"Raes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pieter","family":"Monsieurs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,3,15]]},"reference":[{"key":"520_CR1","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1126\/science.1146689","volume":"318","author":"JA Huber","year":"2007","unstructured":"Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, et al. Microbial population structures in the deep marine biosphere. Science. 2007;318:97\u2013100.","journal-title":"Science"},{"key":"520_CR2","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/1471-2164-7-57","volume":"7","author":"RA Edwards","year":"2006","unstructured":"Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, et al. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics. 2006;7:57.","journal-title":"BMC Genomics"},{"key":"520_CR3","doi-asserted-by":"publisher","first-page":"12115","DOI":"10.1073\/pnas.0605127103","volume":"103","author":"ML Sogin","year":"2006","unstructured":"Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored \u201crare biosphere\u201d. Proc Natl Acad Sci U S A. 2006;103:12115\u201320.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"520_CR4","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1111\/j.1462-2920.2009.02051.x","volume":"12","author":"V Kunin","year":"2010","unstructured":"Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol. 2010;12:118\u201323.","journal-title":"Environ Microbiol"},{"key":"520_CR5","doi-asserted-by":"publisher","first-page":"e27310","DOI":"10.1371\/journal.pone.0027310","volume":"6","author":"PD Schloss","year":"2011","unstructured":"Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 2011;6:e27310.","journal-title":"PLoS One"},{"key":"520_CR6","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1038\/nmeth.1361","volume":"6","author":"C Quince","year":"2009","unstructured":"Quince C, Lanz\u00e9n A, Curtis TP, Davenport RJ, Hall N, Head IM, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009;6:639\u201341.","journal-title":"Nat Methods"},{"key":"520_CR7","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","volume":"79","author":"JJ Kozich","year":"2013","unstructured":"Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112\u201320.","journal-title":"Appl Environ Microbiol"},{"key":"520_CR8","doi-asserted-by":"publisher","first-page":"i304","DOI":"10.1093\/bioinformatics\/btr251","volume":"27","author":"S Balzer","year":"2011","unstructured":"Balzer S, Malde K, Jonassen I. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics. 2011;27:i304\u20139.","journal-title":"Bioinformatics"},{"key":"520_CR9","doi-asserted-by":"publisher","first-page":"3546","DOI":"10.1093\/nar\/24.18.3546","volume":"24","author":"J Cline","year":"1996","unstructured":"Cline J, Braman JC, Hogrefe HH. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 1996;24:3546\u201351.","journal-title":"Nucleic Acids Res"},{"key":"520_CR10","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1101\/gr.112730.110","volume":"21","author":"BJ Haas","year":"2011","unstructured":"Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21:494\u2013504.","journal-title":"Genome Res"},{"key":"520_CR11","doi-asserted-by":"publisher","first-page":"R143","DOI":"10.1186\/gb-2007-8-7-r143","volume":"8","author":"SM Huse","year":"2007","unstructured":"Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007;8:R143.","journal-title":"Genome Biol"},{"key":"520_CR12","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/1471-2164-12-245","volume":"12","author":"A Gilles","year":"2011","unstructured":"Gilles A, Megl\u00e9cz E, Pech N, Ferreira S, Malausa T, Martin J-F. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics. 2011;12:245.","journal-title":"BMC Genomics"},{"key":"520_CR13","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1101\/gr.5571506","volume":"16","author":"J Dostie","year":"2006","unstructured":"Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299\u2013309.","journal-title":"Genome Res"},{"key":"520_CR14","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1038\/nmeth0910-668b","volume":"7","author":"J Reeder","year":"2010","unstructured":"Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010;7:668\u20139.","journal-title":"Nat Methods"},{"key":"520_CR15","doi-asserted-by":"publisher","first-page":"1889","DOI":"10.1111\/j.1462-2920.2010.02193.x","volume":"12","author":"SM Huse","year":"2010","unstructured":"Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12:1889\u201398.","journal-title":"Environ Microbiol"},{"key":"520_CR16","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/1471-2105-12-38","volume":"12","author":"C Quince","year":"2011","unstructured":"Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011;12:38.","journal-title":"BMC Bioinformatics"},{"key":"520_CR17","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/nmeth.1990","volume":"9","author":"L Bragg","year":"2012","unstructured":"Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods. 2012;9:425\u20136.","journal-title":"Nat Methods"},{"key":"520_CR18","doi-asserted-by":"publisher","first-page":"7537","DOI":"10.1128\/AEM.01541-09","volume":"75","author":"PD Schloss","year":"2009","unstructured":"Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537\u201341.","journal-title":"Appl Environ Microbiol"},{"key":"520_CR19","doi-asserted-by":"publisher","first-page":"e60458","DOI":"10.1371\/journal.pone.0060458","volume":"8","author":"JM Gaspar","year":"2013","unstructured":"Gaspar JM, Thomas WK. Assessing the consequences of denoising marker-based metagenomic data. PLoS One. 2013;8:e60458.","journal-title":"PLoS One"},{"key":"520_CR20","doi-asserted-by":"publisher","first-page":"W394","DOI":"10.1093\/nar\/gkl244","volume":"34","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006;34:W394\u20139.","journal-title":"Nucleic Acids Res"},{"key":"520_CR21","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403\u201310.","journal-title":"J Mol Biol"},{"key":"520_CR22","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673\u201380.","journal-title":"Nucleic Acids Res"},{"key":"520_CR23","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590\u20136.","journal-title":"Nucleic Acids Res"},{"key":"520_CR24","doi-asserted-by":"publisher","first-page":"e8230","DOI":"10.1371\/journal.pone.0008230","volume":"4","author":"PD Schloss","year":"2009","unstructured":"Schloss PD. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One. 2009;4:e8230.","journal-title":"PLoS One"},{"key":"520_CR25","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","volume":"10","author":"RC Edgar","year":"2013","unstructured":"Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996\u20138.","journal-title":"Nat Methods"},{"key":"520_CR26","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","volume":"73","author":"Q Wang","year":"2007","unstructured":"Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261\u20137.","journal-title":"Appl Environ Microbiol"},{"key":"520_CR27","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1145\/1656274.1656278","volume":"11","author":"M Hall","year":"2009","unstructured":"Hall M, National H, Frank E, Holmes G, Pfahringer B, Reutemann P, et al. The WEKA data mining software: an update. SIGKDD Explor. 2009;11:10\u20138.","journal-title":"SIGKDD Explor"},{"key":"520_CR28","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.chemolab.2005.09.003","volume":"81","author":"B \u00dcst\u00fcn","year":"2006","unstructured":"\u00dcst\u00fcn B, Melssen WJ, Buydens LMC. Facilitating the application of Support Vector Regression by using a universal Pearson VII function based kernel. Chemom Intell Lab Syst. 2006;81:29\u201340.","journal-title":"Chemom Intell Lab Syst"},{"key":"520_CR29","doi-asserted-by":"crossref","unstructured":"Platt JC. Fast training of support vector machines using sequential minimal optimization. In Adv. Kernel Methods Support Vector Learn. edited by Sch\u00f6lkopf B, Burges C, Smola A Cambridge: The MIT Press; 1998:185\u2013208.","DOI":"10.7551\/mitpress\/1130.003.0016"},{"key":"520_CR30","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/nar\/gks808","volume":"41","author":"A Klindworth","year":"2013","unstructured":"Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0520-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0520-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0520-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0520-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,8]],"date-time":"2023-08-08T20:15:22Z","timestamp":1691525722000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0520-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,15]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["520"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0520-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,15]]},"assertion":[{"value":"8 August 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 February 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 March 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"88"}}