simMSG

simMSG simulates hybrid genomes from two parental genomes and evaluates ancestry-assignment accuracy using Multiplexed Shotgun Genotyping (MSG) and next-generation sequencing data to inform genetic mapping and introgression analyses.

Key Features:

• Simulation of Hybrid Genomes: Generates in silico hybrids by crossing two parental genomes to produce controlled hybrid genotypes.
• Integration with MSG Pipeline: Produces inputs compatible with the Multiplexed Shotgun Genotyping (MSG) pipeline and supports evaluation of MSG-based genotype calls from next-generation sequencing data.
• Parameter Customization: Allows adjustment of simulation and genotyping parameters prior to MSG analysis.
• Ancestry Assignment Accuracy: Enables assessment of ancestry assignment accuracy by simulating variation in ancestry tract length and the number of ancestry-informative markers.

Scientific Applications:

• Mapping Quantitative Trait Loci (QTL): Uses hybrids with known ancestry to test and validate QTL mapping approaches.
• Genotyping Introgressed Lines: Simulates and evaluates genotyping scenarios for introgressed lines to study gene flow and introgression.
• Admixture Mapping: Simulates admixed genomes to assess methods for admixture mapping in populations with mixed ancestry.

Methodology:

Simulates hybrids by crossing two parental genomes, adjusts simulation and genotyping parameters, runs simulated hybrids through the Multiplexed Shotgun Genotyping (MSG) pipeline, and assesses ancestry-assignment accuracy by varying ancestry tract length and the number of ancestry-informative markers.