In a significant stride towards portable DNA sequencing, researchers have developed a novel hardware-software framework that could revolutionize real-time molecular diagnostics, particularly in the maritime sector. The study, led by Karim Hammad from the Arab Academy for Science, Technology and Maritime Transport in Egypt, introduces a Viterbi-based Hidden Markov Model (HMM) implemented on a custom 64-bit RISC-V core, offering a compelling alternative to power-hungry deep learning models.
Nanopore-based DNA sequencing has gained traction for its ability to deliver real-time results in compact devices. However, the basecalling process—translating raw nanopore signals into nucleotide sequences—has been a computational challenge, demanding substantial power and resources. This has limited the deployment of such technologies in portable or field-scale applications, including maritime environments where power efficiency is crucial.
Hammad and his team tackled this issue by designing an embedded system that integrates a Viterbi-HMM detector on an off-the-shelf Virtex-7 FPGA. The results are promising: the system achieves significant energy efficiency improvements—6.5×, 5.5×, and 4.6×—compared to similar HMM-based detectors on x86 processors, Cortex-A9 ARM systems, and a previously published Rocket-based system, respectively. Moreover, it demonstrates 15× and 2.4× energy efficiency superiority over state-of-the-art deep learning-based detectors, with competitive accuracy and sufficient throughput for field-based genomic surveillance and point-of-care diagnostics.
“This study highlights the practical advantages of classical probabilistic algorithms when tightly integrated with lightweight embedded processors for biosensing applications constrained by energy, size, and latency,” Hammad explained. The implications for the maritime sector are substantial. Portable DNA sequencing could enable real-time monitoring of aquatic ecosystems, rapid detection of pathogens in seafood, and on-site diagnostics for crew health, all while operating efficiently in resource-constrained environments.
The commercial opportunities are equally compelling. The maritime industry could see a surge in demand for compact, energy-efficient DNA sequencing devices tailored for ships, research vessels, and offshore platforms. This could open new avenues for companies specializing in maritime technology and biosensing equipment.
The research, published in the journal Biosensors, underscores the potential of integrating classical algorithms with lightweight processors to overcome the computational challenges of portable DNA sequencing. As the maritime industry continues to embrace advanced technologies, such innovations could play a pivotal role in enhancing operational efficiency and environmental monitoring.
For maritime professionals, this development represents a step towards more sustainable and efficient biosensing solutions, paving the way for a new era of real-time diagnostics at sea.