{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T22:59:04Z","timestamp":1778108344832,"version":"3.51.4"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,12,1]],"date-time":"2016-12-01T00:00:00Z","timestamp":1480550400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,12,1]],"date-time":"2016-12-01T00:00:00Z","timestamp":1480550400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["8U54HD080784"],"award-info":[{"award-number":["8U54HD080784"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex\/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We have developed the Merging and Filtering Tool (MeFiT) to combine these pre-processing steps into one simple, intuitive pipeline. MeFiT invokes CASPER (context-aware scheme for paired-end reads) for merging paired-end reads and provides users the option to quality filter the reads using the traditional average Q-score metric or using a maximum expected error cut-off threshold.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>MeFiT provides an open-source solution that permits users to merge and filter paired end illumina reads. The tool has been implemented in python and the source-code is freely available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/nisheth\/MeFiT\">https:\/\/github.com\/nisheth\/MeFiT<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1358-1","type":"journal-article","created":{"date-parts":[[2016,12,1]],"date-time":"2016-12-01T14:23:53Z","timestamp":1480602233000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":77,"title":["MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing"],"prefix":"10.1186","volume":"17","author":[{"given":"Hardik I.","family":"Parikh","sequence":"first","affiliation":[]},{"given":"Vishal N.","family":"Koparde","sequence":"additional","affiliation":[]},{"given":"Steven P.","family":"Bradley","sequence":"additional","affiliation":[]},{"given":"Gregory A.","family":"Buck","sequence":"additional","affiliation":[]},{"given":"Nihar U.","family":"Sheth","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,12,1]]},"reference":[{"key":"1358_CR1","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1146\/annurev.genom.9.081307.164359","volume":"9","author":"ER Mardis","year":"2008","unstructured":"Mardis ER. Next-generation DNA, sequencing methods. Ann Rev Genomics Hum Genet. 2008;9:387\u2013402.","journal-title":"Ann Rev Genomics Hum Genet"},{"key":"1358_CR2","doi-asserted-by":"publisher","first-page":"7952","DOI":"10.1073\/pnas.0503236102","volume":"102","author":"RW Hyman","year":"2005","unstructured":"Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW. Microbes on the human vaginal epithelium. Proc Natl Acad Sci U S A. 2005;102:7952\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1358_CR3","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1126\/science.1110591","volume":"308","author":"PB Eckburg","year":"2005","unstructured":"Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005;308:1635\u20138.","journal-title":"Science"},{"key":"1358_CR4","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, Arrieta JM, Herndl GJ. 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":"1358_CR5","doi-asserted-by":"publisher","first-page":"2927","DOI":"10.1073\/pnas.0607077104","volume":"104","author":"Z Gao","year":"2007","unstructured":"Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A. 2007;104:2927\u201332.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1358_CR6","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","volume":"449","author":"PJ Turnbaugh","year":"2007","unstructured":"Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449:804\u201310.","journal-title":"Nature"},{"key":"1358_CR7","unstructured":"Illumina: 16S Metagenomics Studies with the MiSeq System. Application Note: Microbial Genomics. http:\/\/www.illumina.com\/content\/dam\/illumina-marketing\/documents\/products\/appnotes\/appnote_16s_sequencing.pdf. Accessed 17 Sept 2016."},{"key":"1358_CR8","doi-asserted-by":"publisher","first-page":"e11840","DOI":"10.1371\/journal.pone.0011840","volume":"28","author":"S Rodrigue","year":"2010","unstructured":"Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW. Unlocking short read sequencing for metagenomics. PLoS One. 2010;28:e11840.","journal-title":"PLoS One"},{"key":"1358_CR9","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","volume":"27","author":"T Mago\u010d","year":"2011","unstructured":"Mago\u010d T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957\u201363.","journal-title":"Bioinformatics"},{"key":"1358_CR10","first-page":"13","volume":"14","author":"AP Masella","year":"2012","unstructured":"Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics. 2012;14:13\u201331.","journal-title":"BMC Bioinformatics"},{"key":"1358_CR11","doi-asserted-by":"publisher","first-page":"2870","DOI":"10.1093\/bioinformatics\/bts563","volume":"28","author":"B Lui","year":"2012","unstructured":"Lui B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R. COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics. 2012;28:2870\u20134.","journal-title":"Bioinformatics"},{"issue":"Suppl 9","key":"1358_CR12","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-15-S9-S10","volume":"15","author":"S Kwon","year":"2014","unstructured":"Kwon S, Lee B, Yoon S. CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing. BMC Bioinformatics. 2014;15 Suppl 9:S10.","journal-title":"BMC Bioinformatics"},{"key":"1358_CR13","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","volume":"38","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solex\/Illumina FASTQ variants. Nucleic Acids Res. 2009;38:1767\u201371.","journal-title":"Nucleic Acids Res"},{"key":"1358_CR14","doi-asserted-by":"publisher","first-page":"2438","DOI":"10.1093\/bioinformatics\/btp429","volume":"25","author":"A Martinez-Alcantara","year":"2009","unstructured":"Martinez-Alcantara A, Ballesteros E, Rojas FM, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y. PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics. 2009;25:2438\u20139.","journal-title":"Bioinformatics"},{"key":"1358_CR15","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.1093\/bioinformatics\/btq281","volume":"26","author":"D Blankenberg","year":"2010","unstructured":"Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team. Manipulation of FATSQ data with Galaxy. Bioinformatics. 2010;26:1783\u20135.","journal-title":"Bioinformatics"},{"key":"1358_CR16","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1186\/1471-2105-11-485","volume":"11","author":"MP Cox","year":"2010","unstructured":"Cox MP, Peterson DA, Biggs PJ. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010;11:485.","journal-title":"BMC Bioinformatics"},{"key":"1358_CR17","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","volume":"27","author":"R Schmieder","year":"2011","unstructured":"Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinfomratics. 2011;27:863\u20134.","journal-title":"Bioinfomratics"},{"key":"1358_CR18","doi-asserted-by":"publisher","first-page":"e30619","DOI":"10.1371\/journal.pone.0030619","volume":"7","author":"RK Patel","year":"2012","unstructured":"Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7:e30619.","journal-title":"PLoS One"},{"key":"1358_CR19","unstructured":"Edgar RC. Average Q score. http:\/\/www.drive5.com\/usearch\/manual\/avgq.html. Accessed 17 September 2016."},{"key":"1358_CR20","doi-asserted-by":"crossref","unstructured":"Fettweis JM, Alves JP, Borzelleca JF, Brooks JP, Friedline CJ, Gao Y, Gao X, Girerd P, Harwich MD, Hendricks SL, Jefferson KK, Lee V, Mp H, Neale MC, Puma FA, Reimers MA, Rivera MC, Roberts SB, Serrano MG, Sheth N, Silberg JL, Voegtly L, Prom-Wormley EC, Xie B, York TP, Cornelissen CN, Strauss III JF, Eaves LJ, Buck GA. The Vaginal Microbiome: Disease, genetics and the environment. Nature Proceedings. 2011.","DOI":"10.1038\/npre.2010.5150.1"},{"key":"1358_CR21","doi-asserted-by":"publisher","first-page":"2272","DOI":"10.1099\/mic.0.081034-0","volume":"160","author":"JM Fettweis","year":"2014","unstructured":"Fettweis JM, Brooks JP, Serrano MG, Sheth NU, Girerd PH, Edwards DJ, Strauss JF, Vaginal Microbiome Consortium, Jefferson KK, Buck GA. Differences in vaginal microbiome in African American women versus women of European ancestry. Microbiology. 2014;160:2272\u201382.","journal-title":"Microbiology"},{"key":"1358_CR22","first-page":"276","volume":"10","author":"Integrative HMP (iHMP) Research Network Consortium","year":"2014","unstructured":"Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014;10:276\u201389.","journal-title":"Cell Host Microbe"},{"key":"1358_CR23","unstructured":"Hendrics-Munoz KD, Xu J, Parikh HI, Xu P, Fetweis JM, Kim Y, Louie M, Buck GA, Thacker LR, Sheth NU. Skin-to-skin care and the development of the preterm infant oral microbiome. Am J Perinatol. 2015 [epub ahead of print]."},{"issue":"D1","key":"1358_CR24","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, Peplies J, Gl\u00f6ckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res. 2013;41(D1):D590\u20136.","journal-title":"Nucl Acids Res"},{"key":"1358_CR25","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/j.mimet.2010.08.008","volume":"83","author":"M Hartmann","year":"2010","unstructured":"Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH. V-Xtractor: an open-source, high-throughtput software tool to identify and extract hypervariable regions of small subunit (16S\/18S) ribosomal RNA gene sequences. J Microbiol Methods. 2010;83:250\u20133.","journal-title":"J Microbiol Methods"},{"issue":"Suppl 8","key":"1358_CR26","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1186\/1471-2164-13-S8-S17","volume":"13","author":"JM Fettweis","year":"2012","unstructured":"Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, Brooks JP, Jefferson KK. Vaginal Microbiome Consortium (additional members), Buck GA. Species-level classification of the vaginal microbiome. BMC Genomics. 2012;13 Suppl 8:S17.","journal-title":"BMC Genomics"},{"key":"1358_CR27","doi-asserted-by":"publisher","first-page":"e94","DOI":"10.1093\/nar\/gks251","volume":"40","author":"FE Angly","year":"2012","unstructured":"Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW. Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res. 2012;40:e94.","journal-title":"Nucleic Acids Res"},{"key":"1358_CR28","doi-asserted-by":"publisher","first-page":"R23","DOI":"10.1186\/gb-2009-10-2-r23","volume":"10","author":"JO Korbel","year":"2009","unstructured":"Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009;10:R23.","journal-title":"Genome Biol"},{"key":"1358_CR29","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, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stress B, Thallinger GG, Van Horn DJ, Weber CF. 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"},{"issue":"17","key":"1358_CR30","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(17):5112\u201320.","journal-title":"Appl Environ Microbiol"},{"key":"1358_CR31","first-page":"335","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature. 2010;7:335\u20136.","journal-title":"Nature"},{"key":"1358_CR32","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460\u20131.","journal-title":"Bioinformatics"},{"issue":"21","key":"1358_CR33","doi-asserted-by":"publisher","first-page":"3476","DOI":"10.1093\/bioinformatics\/btv401","volume":"31","author":"RC Edgar","year":"2015","unstructured":"Edgar RC, Flyvbjerg H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics. 2015;31(21):3476\u201382.","journal-title":"Bioinformatics"},{"key":"1358_CR34","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1186\/s13104-016-2172-6","volume":"9","author":"HK Allen","year":"2016","unstructured":"Allen HK, Bayles DO, Looft T, Trachsel J, Bass BE, Alt DP, Bearson SMD, Nicholson T, Casey TA. Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene. BMC Res Notes. 2016;9:380.","journal-title":"BMC Res Notes"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1358-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1358-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1358-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:08:43Z","timestamp":1706810923000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1358-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12,1]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1358"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1358-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,1]]},"assertion":[{"value":"11 June 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 December 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"491"}}