Hardware Accelerated DNA Sequencing
Abstract
DNA sequencing technology is quickly evolving. The latest developments ex-
ploit nanopore sensing and microelectronics to realize real-time, hand-held devices.
A critical limitation in these portable sequencing machines is the requirement of
powerful data processing consoles, a need incompatible with portability and wide
deployment. This thesis proposes a rst step towards addressing this problem, the
construction of specialized computing modules { hardware accelerators { that can
execute the required computations in real-time, within a small footprint, and at a
fraction of the power needed by conventional computers. Such a hardware accel-
erator, in FPGA form, is introduced and optimized specically for the basecalling
function of the DNA sequencing pipeline. Key basecalling computations are identi-
ed and ported to custom FPGA hardware. Remaining basecalling operations are
maintained in a traditional CPU which maintains constant communications with
its FPGA accelerator over the PCIe bus. Measured results demonstrated a 137X
basecalling speed improvement over CPU-only methods while consuming 17X less
power than a CPU-only method.