FR-HIT is a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.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 4 metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, FR-HIT is about 2 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.
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Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li.
FR-HIT, a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.
Bioinformatics. (2011) 27 (12): 1704-1705. doi: 10.1093/bioinformatics/btr252