Instrumenting Genomic Sequence Analysis Pipeline Mothur on Shared Memory Architecture

Abstract

Mothur is an open source bioinformatics pipeline used for biological sequence analysis that has gained increasing attention in the microbial ecology community. Because a large set of functionalities in Mothur are memory bound, it is well suited for shared memory architectures, such as the Nautilus supercomputer. In this paper, we present performance results for several commands in Mothur that are popular in the operational taxonomic unit analysis, and show that Nautilus can accelerate pipeline processes many orders of magnitude faster.