HapCol

HapCol reconstructs haplotypes from sequencing reads to assemble diploid genomes and evaluate the impact of single-nucleotide polymorphisms (SNPs) on phenotypic traits.

Key Features:

• Long Read Compatibility: Optimized for long, gapless reads from sequencing technologies including PacBio RS II (SMRT sequencing) and Oxford Nanopore MinION.
• Error Correction Strategy: Leverages the uniform distribution of sequencing errors and employs an exact algorithm that is exponential in the maximum number of corrections per SNP position to minimize an overall error-correction score.
• Computational Efficiency: Requires less memory and computing resources compared to existing combinatorial methods, enabling processing of higher-coverage datasets without relying on restrictive assumptions such as the all-heterozygous model.
• Performance and Accuracy: Demonstrates competitive accuracy and increased numbers of phased positions, with improved metrics observed on real datasets.
• Scalability: Overcomes limitations related to read length and sequencing coverage to handle larger datasets effectively.

Scientific Applications:

• Genetic analysis of phenotypic traits: Enables reconstruction of haplotypes to study the effects of SNPs on phenotype.
• Personalized medicine: Supports haplotype-resolved variant interpretation relevant to individual genotype-informed treatment strategies.
• Evolutionary biology: Facilitates haplotype-based analyses for studying evolutionary relationships and allele histories.
• Population genetics: Allows phasing of variants at population scale to investigate genetic diversity and structure.

Methodology:

Operates on long, gapless reads and uses an exact, exponential-time algorithm parameterized by the maximum corrections per SNP that minimizes an overall error-correction score while leveraging a uniform sequencing error model and not assuming an all-heterozygous genotype.