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.

FR-HIT first constructs a k-mer hash table for the reference genome sequences. Then for each query, it performs seeding, filtering and banded alignment to identify the alignments to reference sequences that meet user-defined cutoffs.

FR-HIT was written and currently maintained by Dr. Beifang Niu ( in the Dr. Li's group (


(September 2010) fr-hit@GoogleCode is a new Google Code project created for releasing the latest development version of FR-HIT. Usually new minor versions will be released as soon as bug fixings or improvements become available.