A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model

Abstract

Decreasing the cost of high-throughput DNA sequencing technologies, provides a huge amount of data that enables researchers to determine haplotypes for diploid and polyploid organisms. Although various methods have been developed to reconstruct haplotypes in diploid form, their accuracy is still a challenging task. Also, most of the current methods cannot be applied to polyploid form. In this paper, an iterative method is proposed, which employs hypergraph to reconstruct haplotype. The proposed method by utilizing chaotic viewpoint can enhance the obtained haplotypes. For this purpose, a haplotype set was randomly generated as an initial estimate, and its consistency with the input fragments was described by constructing a weighted hypergraph. Partitioning the hypergraph specifies those positions in the haplotype set that need to be corrected. This procedure is repeated until no further improvement could be achieved. Each element of the finalized haplotype set is mapped to a line by chaos game representation, and a coordinate series is defined based on the position of mapped points. Then, some positions with low qualities can be assessed by applying a local projection. Experimental results on both simulated and real datasets demonstrate that this method outperforms most other approaches, and is promising to perform the haplotype assembly.

NCMHap: a novel method for haplotype reconstruction based on Neutrosophic c-means clustering

“…The represented heatmap in Fig. 5, illustrates the reconstruction rate of the proposed method as well as H-PoP [26], SCGD [28], FastHap [25], HGHap [22], AROHap [19], ALTHap [27], and HRCH [29]. The obtained results demonstrate that our method achieves the highest and second-highest RRs for most of the chromosomes.…”

“…7 ALTHap [27] is an iterative algorithm that formulates the haplotype assembly problem as a sparse tensor decomposition. 8 HRCH [29] utilizes a chaotic viewpoint to reconstruct haplotypes. For this aim, the obtained haplotypes are mapped to some coordinate series by applying chaos game representation.…”