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

作者：Beifang Niu, Zhengwei Zhu, LiMin Fu, Sitao Wu, Weizhong Li · 发表于：Bioinformatics · 年份：2011 · DOI：10.1093/bioinformatics/btr252 · 被引用次数：75 · 研究领域：Genomics and Phylogenetic Studies、Genomics and Rare Diseases、Genetics, Bioinformatics, and Biomedical Research

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.