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FPGA-Accelerated 3rd Generation DNA Sequencing


3D Reconstruction in Canonical
Abstract


DNA measurement machines are undergoing an orders-of-magnitude size and power reduction. As a result, the analysis of genetic molecules is increasingly appropriate for mobile platforms. However, sequencing these measurements (converting to the molecule‚??s A-C-G-T text equivalent) requires intense computing resources, a problem for potential realizations as mobile devices. This paper proposes a step towards addressing this issue, the design and implementation of a low-power realtime FPGA hardware accelerator for the basecalling task of nanopore-based DNA measurements. Key basecalling computations are identified and ported to a custom FPGA which operates in tandem with a CPU across a high-speed serial link and a simple API. A measured speed-up over CPU-only basecalling in excess of 100X is realized with an energy efficiency improvement of three orders of magnitude.

KeyWords
DNA sequencing, nanopore, basecalling, FPGA acceleration, HMM, PCIe, RIFFA



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