sgcocaller

sgcocaller generates personalized haplotypes and detects meiotic crossovers from single-gamete (single-cell) DNA sequencing data to enable reconstruction of individualized meiotic crossover landscapes.

Key Features:

• Haplotype phasing: Constructs personalized haplotypes from single-gamete DNA sequencing data, applicable to both high-coverage and low-coverage datasets.
• Crossover calling: Calls meiotic crossovers within individual gametes to map recombination events.
• Low-coverage support: Explicitly handles low depth-of-coverage per gamete, addressing challenges of sparse single-cell sequencing data.
• Scalability and computational efficiency: Implemented for fast processing with minimal memory usage, suitable for large-scale analyses of many gametes.
• Versatility of input: Can be applied to bulk-sequenced samples following additional preprocessing steps to adapt them to single-gamete-style analyses.

Scientific Applications:

• Meiotic recombination mapping: Reconstruction of individualized crossover landscapes for detailed study of recombination patterns.
• Genetic diversity and inheritance studies: Analysis of crossover distributions to inform mechanisms underlying genetic diversity and inheritance patterns.
• Genetic disorder research: Use of phased haplotypes and crossover maps to investigate recombination-related contributions to genetic disorders.
• Evolutionary biology: Comparative analysis of recombination landscapes across individuals or populations to study evolutionary processes.
• Personalized medicine: Generation of individual-specific haplotype and recombination data that can inform precision genetic analyses.

Methodology:

Performs haplotype phasing from single-gamete (single-cell) DNA sequencing data and detects meiotic crossovers per gamete; supports both low-coverage and high-coverage inputs and can accept bulk-sequenced data after additional preprocessing.