XSim: Simulation of Descendants from Ancestors with Sequence Data

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• High-density SNP genotypes are standard for genomic prediction and GWAS.
• There's a growing trend towards using next-generation sequence data for whole-genome analyses.
• Simulation studies are crucial for testing analytical methods in complex genetic scenarios.

Purpose of the Study:

• To develop an efficient software tool for simulating sequence data in descendants within arbitrary pedigrees.
• To provide a method that accommodates complex, multi-generational pedigree structures.

Main Methods:

• Developed XSim software, available in C++ and Julia.
• Implemented a strategy to simulate sequence data by tracking chromosomal segments rather than individual allele states.
• Designed to handle arbitrary and complex pedigree structures.

Main Results:

• XSim enables efficient simulation of sequence data for complex pedigrees.
• The software's segment-based simulation strategy effectively handles intricate family structures.
• Dual C++ and Julia implementations enhance accessibility and performance.

Conclusions:

• XSim is a valuable tool for researchers conducting whole-genome analyses with sequence data.
• The software supports the advancement of genomic prediction and GWAS by enabling realistic data simulation.
• Facilitates the testing and development of analytical methods for complex genetic studies.