QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

• URL: http://arxiv.org/abs/2004.05078v1
• Date: Fri, 10 Apr 2020 15:46:52 GMT
• Title: QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction
• Authors: Aritra Sarkar, Zaid Al-Ars, Koen Bertels
• Abstract summary: We present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly. Details of the implementation are discussed for the various layers of the quantum full-stack accelerator design.
• Score: 2.4192504570921622
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept examples to target both the genomics research community and quantum application developers in a self-contained manner. The details of the implementation are discussed for the various layers of the quantum full-stack accelerator design. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/prince-ph0en1x/QuASeR.

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