Bee_recombination

This repos contains scripts used for reconstructing queen bee haplotypes by sequencing whole genomes of multiple drones of the queen, and for detecting crossover and gene conversion breakpoints.

reconstruct_Queen_haplotype_v2.PB.R

This is an Rscript to reconstruct queen haplotype

CO_NCO_Queen_Drone_postFIlter_v2.R

This is to concatenate LD blocks while filtering out unlikely NCOs

CO_NCO_Queen_Drone_COcount_v1.R

This is to summarise the number of crossovers (COs) and non-crossovers (NCOs)

CO_NCO_Queen_Drone_postFIlter_v4.R

This is a modified script of CO_NCO_Queen_Drone_postFIlter_v2.R to detect gene conversions and NCOs.

Simulate_COInterference_v1.R

This is to investigate the effect of crossover density on the estimate of crossover interference parameter (nu)