We apply matrix completion methods for haplotype assembly from NGS reads to
develop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by
applying a mathematical model to convert the reads to an incomplete matrix and
estimating unknown components. This process is followed by quantizing and
decoding the completed matrix in order to estimate haplotypes. These algorithms
are compared to the state-of-the-art algorithms using simulated data as well as
the real fosmid data. It is shown that the SNP missing rate and the haplotype
block length of the proposed HapOPT are better than those of HapCUT2 with
comparable accuracy in terms of reconstruction rate and switch error rate. A
program implementing the proposed algorithms in MATLAB is freely available at
https://github.com/smajidian/HapMC