FPGA-based DNA Basecalling Hardware Acceleration

Modern DNA sequencing technologies have greatly reduced their physical dimensions while still being able to process large numbers of molecules. Under ideal conditions the raw throughput of such devices may peak at the equivalent of 1 human genome per 3.5 hours. Such outputs present a large burden on the ensuing computing devices tasked with processing the raw data and completing the sequence. To approach the power and spatial footprint of the measurement devices, hardware-accelerated embedded computers are needed. The design of an FPGA-based accelerator customized for one aspect of this task - basecalling - is described herein. Simulations indicate a system capable of basecalling the equivalent of one human genome in 35 minutes within an estimated power budget of 10 W.