A Scalable Hardware Accelerator for Mobile DNA Sequencing

Abstract

DNA sequencers are being miniaturized and increasingly targeted toward mobile applications. However, the intense bioinformatic computing needs of sequencers present a challenge for remote use with limited energy supply. This article presents a step toward realizing a low-power and high-speed bioinformatic engine, a hardware-accelerated basecaller, for mobile sequencing applications. The design is targeted for nanopore-based sequencers and is architected to easily scale to the complexity of this sensor. In addition to accelerating the CPU in real time with a custom field-programmable gate array (FPGA) through a high-speed serial link, the proposed framework envisages the challenging memory requirement of high-order nanopore sensors. The framework proposes a memory management scheme, which provisions the memory requirement problem in three dimensions: the basecalling speed, the circuit's area, and power consumption. The implementation results demonstrate a $142\times $ basecalling speed improvement over a 12-core CPU-only reference, as well as significant speedup compared with other existing solutions. Also, an energy efficiency improvement of three orders of magnitude is measured.