Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments

In this paper, we develop a probabilistic model to approach two realistic scenarios regarding the singular haplotype reconstruction problem--the incompleteness and inconsistency that occurred in the DNA sequencing process to generate the input haplotype fragments, and the common practice used to generate synthetic data in experimental algorithm studies. We design three algorithms in the model that can reconstruct the two unknown haplotypes from the given matrix of haplotype fragments with provable high probability and in linear time in the size of the input matrix. We also present experimental results that conform with the theoretical efficient performance of those algorithms. The software of our algorithms is available for public access and for real-time on-line demonstration.