{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T00:22:50Z","timestamp":1775175770165,"version":"3.50.1"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,7,1]],"date-time":"2015-07-01T00:00:00Z","timestamp":1435708800000},"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\/s12859-015-0595-z","type":"journal-article","created":{"date-parts":[[2015,6,30]],"date-time":"2015-06-30T10:36:44Z","timestamp":1435660604000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":56,"title":["BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS"],"prefix":"10.1186","volume":"16","author":[{"given":"Bruno","family":"Fosso","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica","family":"Santamaria","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marinella","family":"Marzano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Alonso-Alemany","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriel","family":"Valiente","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giacinto","family":"Donvito","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfonso","family":"Monaco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pasquale","family":"Notarangelo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,7,1]]},"reference":[{"issue":"1","key":"595_CR1","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(1):e1.","journal-title":"Nucleic Acids Res"},{"issue":"1\u20133","key":"595_CR2","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/S0166-218X(96)00066-2","volume":"71","author":"WR Pearson","year":"1996","unstructured":"Pearson WR, Robins G, Wrege DE, Zhang TT. On the primer selection problem in polymerase chain reaction experiments. Discrete Appl Math. 1996;71(1\u20133):231\u201346.","journal-title":"Discrete Appl Math"},{"key":"595_CR3","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/1471-2105-13-92","volume":"13","author":"AL Bazinet","year":"2012","unstructured":"Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinformatics. 2012;13:92.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"595_CR4","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1093\/bib\/bbs036","volume":"13","author":"M Santamaria","year":"2012","unstructured":"Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, et al. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform. 2012;13(6):682\u201395.","journal-title":"Brief Bioinform"},{"key":"595_CR5","unstructured":"FastQC [http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/]"},{"key":"595_CR6","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"},{"issue":"3","key":"595_CR7","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(3):403\u201310.","journal-title":"J Mol Biol"},{"issue":"4","key":"595_CR8","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357\u20139.","journal-title":"Nat Methods"},{"issue":"1","key":"595_CR9","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1093\/bioinformatics\/btt256","volume":"30","author":"D Alonso-Alemany","year":"2014","unstructured":"Alonso-Alemany D, Barre A, Beretta S, Bonizzoni P, Nikolski M, Valiente G. Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinformatics. 2014;30(1):17\u201323.","journal-title":"Bioinformatics"},{"key":"595_CR10","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2105-12-8","volume":"12","author":"JC Clemente","year":"2011","unstructured":"Clemente JC, Jansson J, Valiente G. Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics. 2011;12:8.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"595_CR11","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335\u20136.","journal-title":"Nat Methods"},{"issue":"23","key":"595_CR12","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(23):7537\u201341.","journal-title":"Appl Environ Microbiol"},{"issue":"7","key":"595_CR13","doi-asserted-by":"publisher","first-page":"e2836","DOI":"10.1371\/journal.pone.0002836","volume":"3","author":"AF Andersson","year":"2008","unstructured":"Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One. 2008;3(7):e2836.","journal-title":"PLoS One"},{"issue":"Database issue","key":"595_CR14","doi-asserted-by":"publisher","first-page":"D141","DOI":"10.1093\/nar\/gkn879","volume":"37","author":"JR Cole","year":"2009","unstructured":"Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(Database issue):D141\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"595_CR15","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069\u201372.","journal-title":"Appl Environ Microbiol"},{"issue":"Database issue","key":"595_CR16","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","volume":"40","author":"S Federhen","year":"2012","unstructured":"Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012;40(Database issue):D136\u201343.","journal-title":"Nucleic Acids Res"},{"key":"595_CR17","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/1471-2105-11-24","volume":"11","author":"J Huerta-Cepas","year":"2010","unstructured":"Huerta-Cepas J, Dopazo J, Gabaldon T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics. 2010;11:24.","journal-title":"BMC Bioinformatics"},{"issue":"21","key":"595_CR18","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","volume":"27","author":"T Magoc","year":"2011","unstructured":"Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957\u201363.","journal-title":"Bioinformatics"},{"issue":"19","key":"595_CR19","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(19):2460\u20131.","journal-title":"Bioinformatics"},{"key":"595_CR20","unstructured":"Trim Galore! [http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/]"},{"issue":"Web Server issu","key":"595_CR21","doi-asserted-by":"publisher","first-page":"W88","DOI":"10.1093\/nar\/gks497","volume":"40","author":"D Arndt","year":"2012","unstructured":"Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, et al. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 2012;40(Web Server issue):W88\u201395.","journal-title":"Nucleic Acids Res"},{"key":"595_CR22","doi-asserted-by":"crossref","unstructured":"Donvito G, Vicario S, Notarangelo P, Balech B: The BioVeL Project: Robust phylogenetic workflows running on the GRID. In: EGI Community Forum 2012\/EMI Second Technical Conference. 2012.","DOI":"10.22323\/1.162.0029"},{"key":"595_CR23","unstructured":"Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. In: Ausubel FM et al., editors. Current protocols in molecular biology, vol. 19. 2010. Unit 19 10 11\u201321."},{"issue":"10","key":"595_CR24","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1101\/gr.4086505","volume":"15","author":"B Giardine","year":"2005","unstructured":"Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15(10):1451\u20135.","journal-title":"Genome Res"},{"issue":"8","key":"595_CR25","doi-asserted-by":"publisher","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","volume":"11","author":"J Goecks","year":"2010","unstructured":"Goecks J, Nekrutenko A, Taylor J, Galaxy T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86.","journal-title":"Genome Biol"},{"issue":"Database issue","key":"595_CR26","doi-asserted-by":"publisher","first-page":"D643","DOI":"10.1093\/nar\/gkt1209","volume":"42","author":"P Yilmaz","year":"2014","unstructured":"Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks. Nucleic Acids Res. 2014;42(Database issue):D643\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"595_CR27","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1111\/j.1469-8137.2009.03160.x","volume":"186","author":"K Abarenkov","year":"2010","unstructured":"Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S, et al. The UNITE database for molecular identification of fungi\u2013recent updates and future perspectives. New Phytol. 2010;186(2):281\u20135.","journal-title":"New Phytol"},{"issue":"Database issue","key":"595_CR28","doi-asserted-by":"publisher","first-page":"D61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35(Database issue):D61\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"595_CR29","doi-asserted-by":"publisher","first-page":"D5","DOI":"10.1093\/nar\/gkn741","volume":"37","author":"EW Sayers","year":"2009","unstructured":"Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009;37(Database issue):D5\u201315.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"595_CR30","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1093\/bioinformatics\/16.5.439","volume":"16","author":"G Pesole","year":"2000","unstructured":"Pesole G, Liuni S, D'Souza M. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics. 2000;16(5):439\u201350.","journal-title":"Bioinformatics"},{"issue":"13","key":"595_CR31","doi-asserted-by":"publisher","first-page":"3608","DOI":"10.1093\/nar\/gkg548","volume":"31","author":"G Grillo","year":"2003","unstructured":"Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G. PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 2003;31(13):3608\u201312.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"595_CR32","doi-asserted-by":"publisher","first-page":"e1000711","DOI":"10.1371\/journal.ppat.1000711","volume":"6","author":"B Stecher","year":"2010","unstructured":"Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010;6(1):e1000711.","journal-title":"PLoS Pathog"},{"issue":"13","key":"595_CR33","doi-asserted-by":"publisher","first-page":"2642","DOI":"10.1002\/ece3.1107","volume":"4","author":"M Balint","year":"2014","unstructured":"Balint M, Schmidt PA, Sharma R, Thines M, Schmitt I. An Illumina metabarcoding pipeline for fungi. Ecol evol. 2014;4(13):2642\u201353.","journal-title":"Ecol evol"},{"issue":"4","key":"595_CR34","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"WC Huang","year":"2012","unstructured":"Huang WC, Li LP, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28(4):593\u20134.","journal-title":"Bioinformatics"},{"issue":"18","key":"595_CR35","doi-asserted-by":"publisher","first-page":"i420","DOI":"10.1093\/bioinformatics\/btq365","volume":"26","author":"S Balzer","year":"2010","unstructured":"Balzer S, Malde K, Lanzen A, Sharma A, Jonassen I. Characteristics of 454 pyrosequencing data\u2013enabling realistic simulation with flowsim. Bioinformatics. 2010;26(18):i420\u20135.","journal-title":"Bioinformatics"},{"key":"595_CR36","doi-asserted-by":"crossref","unstructured":"Manzari C, Fosso B, Marzano M, Annese A, Caprioli R, D\u2019Erchia AM, et al. The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biological Invasions 2015, (in press).","DOI":"10.1007\/s10530-014-0810-2"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0595-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0595-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0595-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0595-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T15:57:33Z","timestamp":1630598253000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0595-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,7,1]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["595"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0595-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,7,1]]},"assertion":[{"value":"3 March 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"203"}}