title: MPI-blastn and NCBI-TaxCollector: improving metagenomic analysis with high performance classification and wide taxonomic attachment.
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.
authors: Department of Microbiology and Cell Science, University of Florida, Florida, United States.
authors: R
authors: R
authors: Dias
authors: M G
authors: MG
authors: Xavier
authors: F D
authors: FD
authors: Rossi
authors: M V
authors: MV
authors: Neves
authors: T A P
authors: TA
authors: Lange
authors: A
authors: A
authors: Giongo
authors: C A F
authors: CA
authors: De Rose
authors: E W
authors: EW
authors: Triplett
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data; D006801:Humans; D056186:Metagenomics / Q000379:methods / Q000706:statistics & numerical data*; D064307:Microbiota / Q000235:genetics; D012984:Software
keywords: BLAST; NCBI; TaxCollector; metagenomics; sequence alignment; taxonomic attachment; taxonomy assignment