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.
Cite
@article{arxiv.2004.05078,
title = {QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction},
author = {Aritra Sarkar and Zaid Al-Ars and Koen Bertels},
journal= {arXiv preprint arXiv:2004.05078},
year = {2021}
}