FR-HIT，一个快速招募宏基因组reads 到同源参考基因组的程序。
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.
机构信息
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA.
出版信息
Bioinformatics. 2011 Jun 15;27(12):1704-5. doi: 10.1093/bioinformatics/btr252. Epub 2011 Apr 19.
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
摘要
片段招募是将测序reads 与参考基因组对齐的过程，是宏基因组数据分析的关键步骤。现有的序列比对程序要么速度较慢，要么不足以招募宏基因组reads。我们实现了一种高效的算法 FR-HIT 用于片段招募。我们应用 FR-HIT 和其他几种工具，包括 BLASTN、MegaBLAST、BLAT、LAST、SSAHA2、SOAP2、BWA 和 BWA-SW，对来自不同类型测序仪的四个宏基因组数据集进行了招募。平均而言，FR-HIT 和 BLASTN 招募的reads 明显多于其他程序，而 FR-HIT 的速度比 BLASTN 快两个数量级。FR-HIT 比最快的 SOAP2、BWA 和 BWA-SW 慢，但它招募的reads 多 1-5 倍。
可用性
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