A Scalable Hardware Accelerator for Mobile DNA Sequencing
Karim Hammad, Zhongpan Wu, Ebrahim Ghafar‐Zadeh, Sebastian Magierowski
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.