{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T21:38:27Z","timestamp":1776461907388,"version":"3.51.2"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,12,8]],"date-time":"2017-12-08T00:00:00Z","timestamp":1512691200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100006488","name":"French National Institute for Agricultural Research","doi-asserted-by":"publisher","award":["31000553"],"award-info":[{"award-number":["31000553"]}],"id":[{"id":"10.13039\/501100006488","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and instructions for installation: https:\/\/github.com\/geraldinepascal\/FROGS.git. A companion website: http:\/\/frogs.toulouse.inra.fr.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx791","type":"journal-article","created":{"date-parts":[[2017,12,5]],"date-time":"2017-12-05T12:33:26Z","timestamp":1512477206000},"page":"1287-1294","source":"Crossref","is-referenced-by-count":726,"title":["FROGS: Find, Rapidly, OTUs with Galaxy Solution"],"prefix":"10.1093","volume":"34","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Escudi\u00e9","sequence":"first","affiliation":[{"name":"Bioinformatics platform Toulouse Midi-Pyrenees, MIAT, INRA Auzeville CS, Castanet Tolosan cedex, France"}]},{"given":"Lucas","family":"Auer","sequence":"additional","affiliation":[{"name":"INRA, UMR 1136, Universit\u00e9 de Lorraine, INRA-Nancy, Champenoux, France"}]},{"given":"Maria","family":"Bernard","sequence":"additional","affiliation":[{"name":"GABI, INRA, AgroParisTech, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France"}]},{"given":"Mahendra","family":"Mariadassou","sequence":"additional","affiliation":[{"name":"MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France"}]},{"given":"Laurent","family":"Cauquil","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France"}]},{"given":"Katia","family":"Vidal","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France"}]},{"given":"Sarah","family":"Maman","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France"}]},{"given":"Guillermina","family":"Hernandez-Raquet","sequence":"additional","affiliation":[{"name":"Laboratoire d'ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s-LISBP, Universit\u00e9 de Toulouse, INSA, INRA, CNRS, Toulouse, France"}]},{"given":"Sylvie","family":"Combes","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France"}]},{"given":"G\u00e9raldine","family":"Pascal","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France"}]}],"member":"286","published-online":{"date-parts":[[2017,12,7]]},"reference":[{"key":"2023012713011549200_btx791-B1","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/femsre\/fuv050","article-title":"The microbial genomics of arsenic","volume":"40","author":"Andres","year":"2016","journal-title":"FEMS Microbiol. 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