Opto-Aligner: Optical Near-Sensor Architecture for Accelerating DNA Pre-Alignment Filtering

Sequence alignment, a cornerstone application in bioinformatics, is critical for enabling personalized medicine and disease diagnostics. However, the rapid growth of genomic data has led to significant computational challenges, including limited throughput, high latency, and excessive data movement in current sequencing solutions. To address these issues, we propose Opto-Aligner, a high-performance and energy-efficient optical near-sensor accelerator framework tailored for multiple genetic tasks, mainly as DNA/RNA pre-alignment filtering in hyperdimensional space. Opto-Aligner harnesses Silicon Photonics’ promising efficiency and hyperdimensional computing (HDC) robustness to accelerate genome sequence alignment directly at the sensor level. We develop innovative microarchitectural and circuit-level solutions, including specialized hardware partitioning and mapping strategies, to overcome challenges inherent in photonic computing—our cross-layer design accounts for photonic device variability and noise, optimizing HDC algorithms for optical hardware constraints. Opto-Aligner significantly improves throughput and energy efficiency over leading electronic DNA aligners. Relative to the best published electronic aligner (BioHD-HAM), Opto-Aligner delivers a 5.7× higher single-die throughput (0.93Mbs<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> vs. 0.163Mbs<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup>) and a 3.0×10<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup>-fold reduction in energy–delay product, all with sub-nanosecond comparator latency and seamless scaling to multi-bit precision. Opto-Aligner effectively bridges the gap between the computational demands of genome alignment and the limitations of optical hardware.