QuASeR

QuASeR performs reference-free de novo DNA sequence reconstruction by mapping assembly to combinatorial optimization problems and solving them using quantum algorithms and quantum annealing.

Key Features:

• Quantum Computation Platforms: Operates on gate-based quantum simulators and quantum annealing platforms, including the D-Wave system.
• De Novo Assembly Process: Implements a four-step approach using the Traveling Salesman Problem (TSP), Quadratic Unconstrained Binary Optimization (QUBO), Hamiltonian encodings, and the Quantum Approximate Optimization Algorithm (QAOA).
• Proof-of-Concept Examples: Provides examples that demonstrate execution from sets of DNA reads to reconstructed sequences on both simulated and actual quantum hardware.

Scientific Applications:

• Genomics Research: Supports reference-free genome assembly workflows for cases where reference genomes are unavailable or incomplete.
• Quantum Computing Development: Enables exploration and evaluation of quantum algorithms (e.g., QAOA) and quantum annealing approaches applied to biological sequence assembly.

Methodology:

Maps de novo assembly instances to the Traveling Salesman Problem, formulates them as QUBO, encodes solutions with Hamiltonians, and applies QAOA; execution targets gate-based quantum simulators and quantum annealing platforms (including D-Wave) with proof-of-concept end-to-end examples from DNA reads to reconstructed sequences.