Reconfigurable hardware-based genome aligner using quality scores

Smith Waterman Algorithm is a widely used tool in bioinformatics to align reads from aligning to a reference in whole genome sequencing. Mapping millions of sequences read from sequencing is a computationally expensive operation. Accuracy and performance are two important aspects of this process. FPGA based solutions are widely studied. In this paper we tried to achieve a better mapping accuracy for optimum alignment using quality scores of the bases of read sequences while keeping the performance high. We are offering a new Smith Waterman processing unit and systolic array based on quality scores.