FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
Identifieur interne : 000211 ( Ncbi/Checkpoint ); précédent : 000210; suivant : 000212FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
Auteurs : Beifang Niu ; Zhengwei Zhu ; Limin Fu ; Sitao Wu ; Weizhong LiSource :
- Bioinformatics [ 1367-4803 ] ; 2011.
Abstract
Url:
DOI: 10.1093/bioinformatics/btr252
PubMed: 21505035
PubMed Central: 3106194
Affiliations:
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<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
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<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
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<author><name sortKey="Fu, Limin" sort="Fu, Limin" uniqKey="Fu L" first="Limin" last="Fu">Limin Fu</name>
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<author><name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
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<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes</title>
<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
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<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
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<author><name sortKey="Fu, Limin" sort="Fu, Limin" uniqKey="Fu L" first="Limin" last="Fu">Limin Fu</name>
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<author><name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
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<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2011">2011</date>
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<front><div type="abstract" xml:lang="en"><p><bold>Summary:</bold>
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 1–5 times more reads.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://weizhongli-lab.org/frhit">http://weizhongli-lab.org/frhit</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>liwz@sdsc.edu</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btr252/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
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