BHap: a novel approach for bacterial haplotype reconstruction.

ABSTRACT:

Motivation

The bacterial haplotype reconstruction is critical for selecting proper treatments for diseases caused by unknown haplotypes. Existing methods and tools do not work well on this task, because they are usually developed for viral instead of bacterial populations.

Results

In this study, we developed BHap, a novel algorithm based on fuzzy flow networks, for reconstructing bacterial haplotypes from next generation sequencing data. Tested on simulated and experimental datasets, we showed that BHap was capable of reconstructing haplotypes of bacterial populations with an average F1 score of 0.87, an average precision of 0.87 and an average recall of 0.88. We also demonstrated that BHap had a low susceptibility to sequencing errors, was capable of reconstructing haplotyp

SUBMITTER: Li X 

PROVIDER: S-EPMC6931272 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature