NGS Based Haplotype Assembly Using Matrix Completion

Code

• github.com/smajidian/HapMC
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Abstract

We use 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 is followed by quantizing and decoding the completed matrix in order to generate haplotypes. These algorithms are compared to the recently addressed SDhaP algorithm for the real fosmid data. It is shown that reconstruction rate and the MSE of these algorithms outperform the SDhaP. Also, the MEC score of the HapOPT is lower than that of the SDhaP with almost the same running time.

Tasks

Reproductions