Accelerating Genomics Research with OpenCL™ and FPGAs

With the emergence of second-generation sequencing equipment, gene sequencing costs have decreased rapidly, leading to a dramatic increase in the availability of genome sequence data. Correlating the variations in genomes enables advances in a wide range of medical research, including personalized care. Because each human genome comprises over three billion base pairs, whole genomic sequencing requires significant processing power, storage capacity, and network bandwidth. In particular, variant calling is an extremely computationally intensive function. The Genome Analysis Toolkit (GATK) is a software package developed at the Broad Institute to analyze high-throughput sequencing data. This paper describes the acceleration of the GATK’s Haplotype Caller algorithm using Altera®, now part of Intel, FPGAs programmed with Altera’s SDK for OpenCL.