{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T05:41:44Z","timestamp":1775713304909,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","funder":[{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["IIS-1302134, IIS-1526742"],"award-info":[{"award-number":["IIS-1302134, IIS-1526742"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Summary: The growing number of metagenomic studies in medicine and environmental sciences is creating increasing demands on the computational infrastructure designed to analyze these very large datasets. Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e. the number of reads correctly classified). Here we introduce CLARK-S, a new software tool that can classify short reads with high precision, high sensitivity and high speed.<\/jats:p>\n                  <jats:p>Availability and Implementation: CLARK-S is freely available at http:\/\/clark.cs.ucr.edu\/<\/jats:p>\n                  <jats:p>Contact: \u00a0stelo@cs.ucr.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw542","type":"journal-article","created":{"date-parts":[[2016,8,18]],"date-time":"2016-08-18T21:19:13Z","timestamp":1471555153000},"page":"3823-3825","source":"Crossref","is-referenced-by-count":132,"title":["Higher classification sensitivity of short metagenomic reads with CLARK-\n                    <i>S<\/i>"],"prefix":"10.1093","volume":"32","author":[{"given":"Rachid","family":"Ounit","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA"}]},{"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,8,18]]},"reference":[{"key":"2023020114105930400_btw542-B1","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.cels.2015.01.001","article-title":"Geospatial resolution of human and bacterial diversity with city-scale metagenomics","volume":"1","author":"Afshinnekoo","year":"2015","journal-title":"Cell Syst"},{"key":"2023020114105930400_btw542-B2","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1142\/S0219720004000983","article-title":"A tutorial of recent developments in the seeding of local alignment","volume":"2","author":"Brown","year":"2004","journal-title":"J. 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Microbiol"},{"key":"2023020114105930400_btw542-B10","article-title":"Metagenomic covariation along densely sampled environmental gradients in the red sea","author":"Thompson","year":"2016","journal-title":"ISME J"},{"key":"2023020114105930400_btw542-B11","doi-asserted-by":"crossref","first-page":"R46.","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/24\/3823\/49027269\/bioinformatics_32_24_3823.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/24\/3823\/49027269\/bioinformatics_32_24_3823.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:01:55Z","timestamp":1675278115000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/24\/3823\/2525654"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,18]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2016,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw542","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/053462","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,12,15]]},"published":{"date-parts":[[2016,8,18]]}}}