high performance computing on graphics processing units: hgpu.org

With the rapid decrease in gene sequencing costs due to the emergence of second-generation sequencing equipment, the availability of genome sequence data is increasing dramatically. The ability to correlate the variations among genomes is enabling advances in a wide range of medical research and personalized care. Because each human genome comprises more than three billion base pairs, whole genomic sequencing requires significant processing power, storage capacity, and network bandwidth. In particular, variant calling is extremely computationally intensive. 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 HaplotypeCaller algorithm using Intel’s field programmable gate array (FPGA) devices, programmed using the Intel FPGA SDK for OpenCL technology.