QuASeR

Quantum Accelerated de novo DNA sequence reconstruction

Journal Article (2021)
Author(s)

A. Sarkar (TU Delft - QCD/Feld Group)

Zaid Al-Ars (TU Delft - Quantum & Computer Engineering, TU Delft - Computer Engineering)

Koen Bertels (Universidade do Porto, TU Delft - QCD/Almudever Lab)

Research Group
Computer Engineering
Copyright
© 2021 A. Sarkar, Z. Al-Ars, K.L.M. Bertels
DOI related publication
https://doi.org/10.1371/journal.pone.0249850
More Info
expand_more
Publication Year
2021
Language
English
Copyright
© 2021 A. Sarkar, Z. Al-Ars, K.L.M. Bertels
Research Group
Computer Engineering
Issue number
4 April
Volume number
16
Reuse Rights

Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons.

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. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with a proof-of-concept example to target both the genomics research community and quantum application developers in a self-contained manner. The implementation and results on executing the algorithm from a set of DNA reads to a reconstructed sequence, on a gate-based quantum simulator, the D-Wave quantum annealing simulator and hardware are detailed. 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/QE-Lab/QuASeR.