High Performance Linkage Disequilibrium: Fpgas Hold The Key

DNA sequencing technologies allow the rapid sequencing of full genomes in a cost-effective way, leading to ever-growing genomic datasets that comprise thousands of genomes and millions of genetic variants. In population genomics and genome-wide association studies, widely used statistics such as linkage disequilibrium become computationally demanding when thousands of whole genomes are investigated. Long analysis times and excessive memory requirements usually prevent researchers from conducting exhaustive analyses, sacrificing the ability to detect distant genetic associations. In this work, we describe a generic algorithmic approach for organizing arbitrarily distant computations on full genomes, and to offload operations from the host processor to accelerators. We explore FPGAs as accelerators for linkage disequilibrium because the bulk of required operations are discrete, making them a good fit for reconfigurable fabric. We describe a versatile and trivially expandable architecture, and develop an automatic RTL generation software to search the design space. We find that, when thousands of genomes from complex species such as humans, are analyzed, current FPGAs can achieve up to 50X faster processing than state-of-the-art software running on multi-core workstations.