NanoCross

NanoCross detects recombinant crossover events in eukaryotic genomes using Oxford Nanopore Technologies (ONT) long-read sequencing to map meiotic recombination and construct high-resolution recombination maps.

Key Features:

• Error Reduction: Reduces sequencing errors inherent in ONT reads to improve accuracy of downstream analyses.
• Haplotype Construction: Constructs individual haplotypes from homopolymer-filtered ONT sequences.
• Recombination Event Detection: Analyzes individual molecule reads to estimate cross-recombinant (crossover) events leveraging ONT long-read resolution.
• Sensitivity and Specificity: Simulations demonstrate maintained balance between sensitivity and specificity under moderate heterozygous variation density and adequate sequencing depth.
• High-Resolution Recombination Mapping: Facilitates construction of high-resolution recombination maps for individual genomes, exemplified by application to wild boar and comparisons with male breeding pig populations.

Scientific Applications:

• Recombination Mapping: Generation of detailed meiotic recombination maps for individual genomes using ONT data.
• Evolutionary Genetics: Investigation of genetic diversity and the molecular basis of meiotic recombination across taxa.
• Comparative Genomics: Comparison of recombination landscapes between populations or species, such as wild boar versus breeding pigs.
• Rate Variation Studies: Analysis of how recombination rates vary and what genomic or population factors influence those variations.

Methodology:

Computational steps explicitly stated include error reduction of ONT sequences, haplotype construction from homopolymer-filtered reads, estimation of cross-recombinant events from individual molecule reads, and validation by simulations.