RT Journal Article
SR Electronic
T1 Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.06.371799
DO 10.1101/2020.11.06.371799
A1 Jim Shaw
A1 Yun William Yu
YR 2021
UL http://biorxiv.org/content/early/2021/04/30/2020.11.06.371799.abstract
AB Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem. We introduce two new mathematical formulations of polyploid haplotype phasing: (1) the min-sum max tree partition (MSMTP) problem, which is a more flexible graphical metric compared to the standard minimum error correction (MEC) model in the polyploid setting, and (2) the uniform probabilistic error minimization (UPEM) model, which is a probabilistic analogue of the MEC model. We incorporate both formulations into a long-read based polyploid haplotype phasing method called flopp. We show that flopp compares favorably to state-of-the-art algorithms—up to 30 times faster with 2 times fewer switch errors on 6x ploidy simulated data.Competing Interest StatementThe authors have declared no competing interest.