Haplotype assembly using Riemannian trust-region method

Abstract We model the Haplotype Assembly Problem (HAP) as a minimization problem over an ( n − 1 ) -dimensional sphere, where n is the haplotype length. A manifold optimization approach is proposed to solve this problem. To escape the saddle points, the Riemannian trust region method is utilized and its convergence is proved. Simulation results over both real and synthetic data show that the proposed method is considerably accurate for haplotype estimation.