{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T06:58:56Z","timestamp":1771916336075,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1993,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis. The available sequence alignment programs are either slow or insufficient for recruiting metagenomic reads. We implemented an efficient algorithm, FR-HIT, for fragment recruitment. We applied FR-HIT and several other tools including BLASTN, MegaBLAST, BLAT, LAST, SSAHA2, SOAP2, BWA and BWA-SW to recruit four metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, while FR-HIT is about two orders of magnitude faster than BLASTN. FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1\u20135 times more reads.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/weizhongli-lab.org\/frhit.<\/jats:p>\n               <jats:p>Contact: \u00a0liwz@sdsc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr252","type":"journal-article","created":{"date-parts":[[2011,4,20]],"date-time":"2011-04-20T04:06:58Z","timestamp":1303272418000},"page":"1704-1705","source":"Crossref","is-referenced-by-count":62,"title":["FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes"],"prefix":"10.1093","volume":"27","author":[{"given":"Beifang","family":"Niu","sequence":"first","affiliation":[{"name":"Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA"}]},{"given":"Zhengwei","family":"Zhu","sequence":"additional","affiliation":[{"name":"Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA"}]},{"given":"Limin","family":"Fu","sequence":"additional","affiliation":[{"name":"Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA"}]},{"given":"Sitao","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA"}]},{"given":"Weizhong","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,4,19]]},"reference":[{"key":"2023012511142453800_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012511142453800_B2","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1145\/299432.299460","article-title":"q-gram based database searching using a suffix array (QUASAR)","volume":"99","author":"Burkhardt","year":"1999","journal-title":"RECOMB"},{"key":"2023012511142453800_B3","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1007\/3-540-54345-7_67","article-title":"2 Algorithms for approximate string matching in static texts","volume":"520","author":"Jokinen","year":"1991","journal-title":"Lect. 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