CyberinfraV1, Main, Exploration, bibRecord, 000695

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

Identifieur interne : 000695 ( Main/Exploration ); précédent : 000694; suivant : 000696

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

Affiliations:

Le document en format XML

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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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<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>
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<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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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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