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FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

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FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

Auteurs : Beifang Niu ; Zhengwei Zhu ; Limin Fu ; Sitao Wu ; Weizhong Li

Source :

Bioinformatics [ 1367-4803 ] ; 2011.

RBID : PMC:3106194

Abstract

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 1–5 times more reads.

Availability: http://weizhongli-lab.org/frhit.

Contact: liwz@sdsc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106194

DOI: 10.1093/bioinformatics/btr252
PubMed: 21505035
PubMed Central: 3106194

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PMC:3106194

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<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
</author>
<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
</author>
<author><name sortKey="Fu, Limin" sort="Fu, Limin" uniqKey="Fu L" first="Limin" last="Fu">Limin Fu</name>
</author>
<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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<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="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
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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>
</div>
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<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
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  <front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
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<issn pub-type="ppub">1367-4803</issn>
<issn pub-type="epub">1367-4811</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
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<article-meta><article-id pub-id-type="pmid">21505035</article-id>
<article-id pub-id-type="pmc">3106194</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/btr252</article-id>
<article-id pub-id-type="publisher-id">btr252</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Applications Note</subject>
<subj-group><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Niu</surname>
<given-names>Beifang</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Zhu</surname>
<given-names>Zhengwei</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Fu</surname>
<given-names>Limin</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Sitao</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Weizhong</given-names>
</name>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
</contrib-group>
<aff>Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA</aff>
<author-notes><corresp id="COR1">*To whom correspondence should be addressed.</corresp>
<fn><p>Associate Editor: Martin Bishop</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><day>15</day>
<month>6</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>4</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>19</day>
<month>4</month>
<year>2011</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the 
 							. </pmc-comment>
      <volume>27</volume>
<issue>12</issue>
<fpage>1704</fpage>
<lpage>1705</lpage>
<history><date date-type="received"><day>19</day>
<month>2</month>
<year>2011</year>
</date>
<date date-type="rev-recd"><day>8</day>
<month>4</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>11</day>
<month>4</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2011. Published by Oxford University Press.</copyright-statement>
<copyright-year>2011</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<counts><page-count count="2"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>

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FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

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Abstract

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