{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T11:23:19Z","timestamp":1777634599484,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T00:00:00Z","timestamp":1491523200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The rapidly expanding microbiomics field is generating increasingly larger datasets, characterizing the microbiota in diverse environments. Although classical numerical ecology methods provide a robust statistical framework for their analysis, software currently available is inadequate for large datasets and some computationally intensive tasks, like rarefaction and associated analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness. Our software is designed for ease of use, operating at least 7x faster than existing solutions, despite requiring 10x less memory.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>C\u2009++\u2009and R source code (GPL v.2) as well as binaries are available from https:\/\/github.com\/hildebra\/Rarefaction and from CRAN (https:\/\/cran.r-project.org\/).<\/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\/btx206","type":"journal-article","created":{"date-parts":[[2017,4,5]],"date-time":"2017-04-05T15:01:01Z","timestamp":1491404461000},"page":"2594-2595","source":"Crossref","is-referenced-by-count":117,"title":["RTK: efficient rarefaction analysis of large datasets"],"prefix":"10.1093","volume":"33","author":[{"given":"Paul","family":"Saary","sequence":"first","affiliation":[{"name":"Structural & Computational Biology Unit, EMBL, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristoffer","family":"Forslund","sequence":"additional","affiliation":[{"name":"Structural & Computational Biology Unit, EMBL, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"Structural & Computational Biology Unit, EMBL, Heidelberg, Germany"},{"name":"MMPU, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany"},{"name":"Max Delbr\u00fcck Centre for Molecular Medicine, Berlin, Germany"},{"name":"Department of Bioinformatics, University of W\u00fcrzburg, W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Falk","family":"Hildebrand","sequence":"additional","affiliation":[{"name":"Structural & Computational Biology Unit, EMBL, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"2023020206282717200_btx206-B1","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. 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Model. Comput. Simul"},{"key":"2023020206282717200_btx206-B7","first-page":"631","author":"Oksanen","year":"2007"},{"key":"2023020206282717200_btx206-B8","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol"},{"key":"2023020206282717200_btx206-B9","first-page":"348","article-title":"Structure and function of the global ocean microbiome","volume":"80","author":"Sunagawa","year":"2015","journal-title":"Science"},{"key":"2023020206282717200_btx206-B10","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/16\/2594\/49041222\/bioinformatics_33_16_2594.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/16\/2594\/49041222\/bioinformatics_33_16_2594.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:30:13Z","timestamp":1675319413000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/16\/2594\/3111845"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,4,7]]},"references-count":10,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2017,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx206","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,15]]},"published":{"date-parts":[[2017,4,7]]}}}