QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction
arXiv:2004.05078 · doi:10.1371/journal.pone.0249850
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.
arXiv comment24 pages
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