Banded Pair-HMM Algorithm for DNA Variant Calling and Its Hardware Accelerator Design

In this paper, we propose a new pair hidden Markov model (Pair-HMM) algorithm, namely Banded Pair-HMM, which is a heuristic approach for variant calling applications. When compared to the conventional Pair-HMM, our Banded Pair-HMM can reduce the execution time at a minor cost in accuracy. In addition, a hardware accelerator is implemented using TSMC 40nm technology based on the proposed algorithm. As demonstrated later in the paper, the proposed hardware accelerator runs 4× faster than the conventional Pair-HMM hardware, and over 17,000× faster than the original Pair-HMM software.