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

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 c...

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Bibliographic Details
Published in:PloS one 2020-10, Vol.15 (10), p.e0241291-e0241291
Main Authors: Olyaee, Mohammad Hossein, Khanteymoori, Alireza, Khalifeh, Khosrow
Format: Article
Language:English
Subjects:
Algorithms
Assembly
Computational biology
Computer engineering
Deoxyribonucleic acid
Diploids
DNA
DNA sequencing
Error correction & detection
Gene sequencing
Genetic research
Genome, Human
Genomes
Genomics
Graph theory
Haplotypes
Heuristic
Humans
Iterative methods
Methods
Models, Genetic
Mutation
Polyploidy
Sequence Analysis, DNA
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0241291