Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis

Abstract

BackgroundThe use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts.ResultsIGS was integrated on Maha-Fs (HPC) system, to provide the parallelization required to analyze 2504 whole genomes. Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and SGI-UV300 (solid state drive memory). It was observed that SGI-UV300 was faster, having 32.5 mins of process time, while that of the Maha-Fs was 55.2 mins.ConclusionsThe implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this approach will accelerate research advancement in personalized genomic medicine. Our method is comparable to the fastest methods for sequence alignment.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2499-1) contains supplementary material, which is available to authorized users.