Genome assembly tutorial

Code for the paper Genome assembly using quantum and quantum-inspired annealing

Usage

Example for synthetic data

import numpy as np
import DeBruijnDNA

from dwave.system import LeapHybridSampler
API_KEY = "D-WAVE_OCEAN_SDK_API_KEY"

sequence = 'CATACACCTAA'
kmer_len, suffix_len = 3, 2

adjacency_matrix, node_labels = DeBruijnDNA.make_debr(sequence, kmer_len=kmer_len, suffix_len=suffix_len)
Q = DeBruijnDNA.to_qubo(adjacency_matrix)

q = {}
size = len(Q)
for i in range(size):
    for j in range(size):
        q[(i,j)] = Q[i][j]
            
sampler = LeapHybridSampler(token=API_KEY)
response = sampler.sample_qubo(q)

result = []
for sample, energy in response.data(['sample', 'energy']): 
    result.append(sample)
    result.append(energy)

result.append(response.info) # view timings
spins, energy = [result[0][i] for i in result[0].keys()], result[1]

In spins equal 1 is coded node position in Hamiltonian path i = (spin index) % (sequence length - 2)

For more detailed examples see example.ipynb