nPhase

nPhase phases haplotypes from aligned short-read and long-read sequencing data to produce contiguous, ploidy-agnostic haplotype predictions for polyploid genomes.

Key Features:

• Ploidy Agnosticism: Operates without prior specification of ploidy, enabling analysis across a range of polyploid levels.
• Integration of Read Types: Combines short-read and long-read sequencing reads aligned to a reference genome to improve haplotype precision and contiguity.
• Validation on Model Species: Validated using virtually constructed polyploid genomes of Saccharomyces cerevisiae by combining sequencing data from homozygous isolates to simulate polyploidy.
• High Accuracy and Contiguity: Achieved average accuracy exceeding 95% and produced contiguous haplotigs covering >90% of each chromosome at heterozygosity rates ≥0.5% in validation studies.

Scientific Applications:

• Population Genomics: Provides detailed haplotype information for studying genetic diversity and evolutionary dynamics in polyploid populations.
• Hybrid Studies: Enables investigation of hybridization events and their genomic consequences through accurate phasing of complex genomes.

Methodology:

Algorithm implemented in Python that phases haplotypes by combining short-read and long-read sequencing data aligned to a reference genome, with validation performed using simulated polyploids generated from sequencing data of homozygous Saccharomyces cerevisiae isolates.