Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures

With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.