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Bioinformatics. 2011 Jun 15;27(12):1704-5. doi: 10.1093/bioinformatics/btr252. Epub 2011 Apr 19.

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

Author information

1
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA.

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.

PMID:
21505035
PMCID:
PMC3106194
DOI:
10.1093/bioinformatics/btr252
[Indexed for MEDLINE]
Free PMC Article

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