Dias R, Xavier M G, Rossi F D, Neves M V, Lange T A P, Giongo A, De Rose C A F, Triplett E W
Department of Microbiology and Cell Science, University of Florida, Florida, United States.
J Bioinform Comput Biol. 2014 Jun;12(3):1450013. doi: 10.1142/S0219720014500139.
Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min.
宏基因组测序技术正在迅速发展，多年来高通量基因测序的输出数据量大幅增加。这使我们面临一种需要先进的计算优化来进行宏基因组分析的情况。在本文中，我们描述了核苷酸BLAST的一种新的并行实现（MPI-blastn）以及一种用于对基本局部比对搜索工具（BLAST）结果进行分类归属的新工具，该工具支持美国国立医学图书馆国家生物技术信息中心（NCBI）的分类法（NCBI-TaxCollector）。与mpiBLAST和ScalaBLAST相比，MPI-blastn具有高性能。在我们的最佳情况下，MPI-blastn在384个核心上的运行速度能够快408倍。我们的评估表明，NCBI-TaxCollector进行分类归属的速度比以前的TaxCollector快125倍，所需的随机存取存储器（RAM）少120倍。通过我们的优化，当前需要37小时的多序列搜索可以在不到6分钟内完成，而使用NCBI分类数据归属的后处理原本需要48小时，现在能够在23分钟内运行。
