title: FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://weizhongli-lab.org/frhit.
authors.affiliation: Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA.
authors.forename: Beifang
authors.initials: B
authors.lastname: Niu
authors.forename: Zhengwei
authors.initials: Z
authors.lastname: Zhu
authors.forename: Limin
authors.initials: L
authors.lastname: Fu
authors.forename: Sitao
authors.initials: S
authors.lastname: Wu
authors.forename: Weizhong
authors.initials: W
authors.lastname: Li
mesh_terms: D000465:Algorithms; D016678:Genome; D056186:Metagenomics / Q000379:methods* / Q000592:standards; D012015:Reference Standards; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards; D017422:Sequence Analysis, DNA; D012984:Software