H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

This article models the polyploid haplotyping problem as an optimal poly-partition problem of the reads, called the Polyploid Balanced Optimal Partition model. For the reads sequenced from a k-ploid genome, the model tries to divide the reads into k groups such that the difference between the reads of the same group is minimized while the difference between the reads of different groups is maximized. When the genotype information is available, the model is extended to the Polyploid Balanced Optimal Partition with Genotype constraint problem. These models are all NP-hard. We propose two heuristic algorithms, H-PoP and H-PoPG, based on dynamic programming and a strategy of limiting the number of intermediate solutions at each iteration, to solve the two models, respectively. Extensive experimental results on simulated and real data show that our algorithms can solve the models effectively, and are much faster and more accurate than the recent state-of-the-art polyploid haplotyping algorithms. The experiments also show that our algorithms can deal with long reads and deep read coverage effectively and accurately. Furthermore, H-PoP might be applied to help determine the ploidy of an organism.
Availability and Implementation: https://github.com/MinzhuXie/H-PoPG
Contact: [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - December 18, 2016 Category: Bioinformatics Authors: Xie, M., Wu, Q., Wang, J., Jiang, T. Tags: SEQUENCE ANALYSIS Source Type: research