MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment

被引：7

作者：

Dias, R. ^{[1
]}

Xavier, M. G. ^{[2
]}

Rossi, F. D. ^{[2
]}

Neves, M. V. ^{[2
]}

Lange, T. A. P. ^{[2
]}

Giongo, A. ^{[3
]}

De Rose, C. A. F. ^{[2
]}

Triplett, E. W. ^{[1
]}

机构：

[1] Univ Florida, Dept Microbiol & Cell Sci, Gainesville, FL 32611 USA

[2] Pontiph Catholic Univ Rio Grande Sul, Fac Informat, Porto Alegre, RS, Brazil

[3] Pontiph Catholic Univ Rio Grande Sul, Fac Biosci, Porto Alegre, RS, Brazil

来源：

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY | 2014年 / 12卷 / 03期

关键词：

BLAST; TaxCollector; NCBI; sequence alignment; metagenomics; taxonomy assignment; taxonomic attachment; PROJECT RDP-II; DATABASE;

D O I：

10.1142/S0219720014500139

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

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, MPIblastn 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.

引用

页数：17

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