Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.

ABSTRACT: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as

SUBMITTER: Pulido-Tamayo S 

PROVIDER: S-EPMC4652744 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature