EVORhA

EVORhA reconstructs genome-wide haplotypes from clonal populations by integrating read overlap information and frequency estimations to resolve low-frequency mutations and limited segregating sites.

Key Features:

• Haplotype Reconstruction: Reconstructs genome-wide haplotypes by leveraging read overlap information and frequency estimates of inferred local haplotypes.
• Complementary Phasing Information: Integrates frequency-based information with phasing to improve accuracy when read lengths or numbers of segregating sites are limited.
• Applicability to Low Mutation Frequency Systems: Targets clonal systems with low mutation frequencies and few segregating sites to reduce ambiguity in haplotype phasing.

Scientific Applications:

• Population Composition Analysis: Reconstructs the population composition of evolved bacterial populations to inform evolutionary dynamics.
• Clinical Sample Analysis: Decomposes mixed bacterial infections from clinical samples to resolve constituent haplotypes.

Methodology:

Combines non-empty read overlap data with frequency estimations of inferred local haplotypes to perform phasing and genome-wide haplotype reconstruction.