Bioinformatics is an emerging field with seemingly limitless possibilities for advances in numerous areas of research and applications. We propose an FPGA-based solution to the short read mapping problem, which greatly accelerates the task of aligning short length reads to a known reference genome. We compare the runtime, power consumption, and sensitivity of the hardware system to the BFAST and Bowtie software tools. The described hardware system demonstrates a 129X speedup versus the BFAST software and a 10X speedup versus the Bowtie software. Also, the hardware system is more sensitive than the Bowtie software, which aligns approximately 85% of the short reads, as compared to the 91% aligned by the hardware.