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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment
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MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment

机译：MPI-blastn和NCBI-TaxCollector：通过高性能分类和广泛的分类学附件，改善宏基因组学分析

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摘要

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.
机译：这些年来，元基因组测序技术正在迅速发展，并且高通量基因测序的输出数据量已大大增加。这将我们带到需要高级计算优化来执行宏基因组分析的场景。在本文中，我们描述了核苷酸BLAST（MPI-blastn）的新并行实现方式和用于支持NCBI分类法（NCBI-TaxCollector）的基本局部比对搜索工具（BLAST）结果分类的新工具。与mpiBLAST和ScalaBLAST相比，MPI-blastn具有很高的性能。在最好的情况下，MPI-blastn在384个内核中的运行速度提高了408倍。我们的评估表明，NCBI-TaxCollector能够比以前的TaxCollector更快地执行生物分类附件125倍，所需RAM少120倍。通过我们的优化，当前耗时37小时的多序列搜索可以在不到6分钟的时间内执行，而带有NCBI分类数据附件的后处理（耗时48小时）现在可以在23分钟内运行。

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