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Publication . Article . 2014

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

Dias, R.; Xavier, M. G.; Rossi, F. D.; Neves, M. V.; Lange, T. A. P.; Giongo, A.; De Rose, C. A. F.; +1 Authors
Published: 26 Jun 2014
Publisher: World Scientific Pub Co Pte Lt
Abstract
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.
Subjects by Vocabulary

Microsoft Academic Graph classification: Sequence alignment Biology NCBI Taxonomy Metagenomics Sequence search Basic Local Alignment Search Tool Data mining computer.software_genre computer DNA sequencing

Subjects

Computer Science Applications, Molecular Biology, Biochemistry