PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling.

MOTIVATION

Single-individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes.

RESULTS

Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping. The proposed PEATH method was compared to the most recent algorithms in terms of the phased length, N50 length, switch error rate and minimum error correction. The PEATH algorithm consistently provides the best phase and N50 lengths, as long as possible, given datasets. In addition, verification of the simulation data demonstrated that the PEATH method outperforms other methods on high noisy data. Additionally, the experimental results of a real dataset confirmed that the PEATH method achieved comparable or better accuracy.

AVAILABILITY AND IMPLEMENTATION

Source code of PEATH is available at https://github.com/jcna99/PEATH.

CONTACT

jkrhee@catholic.ac.kr or sooyong.shin@gmail.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.