Accelerating De Novo Genome Assembly via Quantum-Assisted Graph Optimization with Bitstring Recovery

• URL: http://arxiv.org/abs/2602.00156v1
• Date: Thu, 29 Jan 2026 19:03:55 GMT
• Title: Accelerating De Novo Genome Assembly via Quantum-Assisted Graph Optimization with Bitstring Recovery
• Authors: Jaya Vasavi Pamidimukkala, Himanshu Sahu, Ashwini Kannan, Janani Ananthanarayanan, Kalyan Dasgupta, Sanjib Senapati,
• Abstract summary: Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine.<n>De novo genome assembly presents significant challenges due to its high computational complexity, affecting both time and accuracy.<n>We propose a hybrid approach utilizing a quantum computing-based optimization algorithm integrated with classical pre-processing to expedite the genome assembly process.
• Score: 0.0
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome assembly, which involves constructing an entire genome sequence from scratch without a reference genome, presents significant challenges due to its high computational complexity, affecting both time and accuracy. In this study, we propose a hybrid approach utilizing a quantum computing-based optimization algorithm integrated with classical pre-processing to expedite the genome assembly process. Specifically, we present a method to solve the Hamiltonian and Eulerian paths within the genome assembly graph using gate-based quantum computing through a Higher-Order Binary Optimization (HOBO) formulation with the Variational Quantum Eigensolver algorithm (VQE), in addition to a novel bitstring recovery mechanism to improve optimizer traversal of the solution space. A comparative analysis with classical optimization techniques was performed to assess the effectiveness of our quantum-based approach in genome assembly. The results indicate that, as quantum hardware continues to evolve and noise levels diminish, our formulation holds a significant potential to accelerate genome sequencing by offering faster and more accurate solutions to the complex challenges in genomic research.

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