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


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

SUBMITTER: Niu B 

PROVIDER: S-EPMC3106194 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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

Niu Beifang B   Zhu Zhengwei Z   Fu Limin L   Wu Sitao S   Li Weizhong W  

Bioinformatics (Oxford, England) 20110419 12


<h4>Summary</h4>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  ...[more]

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