A Genetic Algorithm for Single Individual SNP Haplotype Assembly

The minimum error correction (MEC) model is one of the widely accepted computational model for single individual haplotype reconstruction problem, and it has been proved to be NP-complete by Lippert et al.. Qian et al. presented a particle swarm optimization (PSO) algorithm to solve the model, and the length of a particle code is equal to the number of fragments. However, there are hundreds and thousands of fragments in practical applications, the PSO algorithm based on this kind of long particle code can not obtain high reconstruction rate efficiently. In this paper, a practical heuristic algorithm based on genetic algorithm (GA) is presented to solve the problem. A kind of short chromosome code and an effective climb operator are designed for the algorithm. Experimental results indicate that the algorithm designed in this paper can get higher reconstruction rate than the PSO algorithm.