Viral haplotype reconstruction from long reads with virCHap.

virCHap achieves up to 96% recall and over 97% accuracy in viral haplotype reconstruction, outperforming existing tools across multiple viral datasets.

• Why it matters: Accurate viral haplotype resolution is essential for understanding viral diversity and developing targeted treatments, but current methods struggle with high similarity, unknown strain numbers, and repetitive regions.
• What they did: The team developed virCHap, a reference-based haplotype phasing algorithm that uses graph partitioning and iterative cluster merging on long-read sequencing data, tested on simulated and real datasets.
• The result: virCHap's superior performance enables more precise viral genome analysis, improving abundance estimates and read clustering, which can advance viral research and therapeutic strategies.