Viral haplotype reconstruction from long reads with virCHap.

virCHap achieves 96% recall in viral haplotype reconstruction, surpassing existing tools by 13.6% on simulated large-genome VZV data.

• Why it matters: Accurate viral haplotype resolution is essential for understanding viral disease prevalence and developing effective treatments, but current methods face challenges like high similarity and unknown strain numbers.
• What they did: The study developed virCHap, a reference-based haplotype phasing algorithm using graph partitioning and iterative cluster merging, tested on simulated and real datasets including VZV, PVY, and SARS-CoV-2.
• The result: virCHap outperforms existing tools with high precision (>94.4%), recall (>97%), and read clustering accuracy (93.4%), enabling more reliable viral genome analysis and abundance estimation.