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

作者：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

来源：Journal of Bioinformatics and Computational Biology, 2014, 12(3): 1450013.

DOI：10.1142/S0219720014500139

• BLAST
• TaxCollector
• NCBI
• sequence alignment
• metagenomics
• taxonomy assignment
• taxonomic attachment

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.

• 出版日期2014-6