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Published on: March 22, 2018
GENOME: a rapid coalescent-based whole genome simulator
Liming Liang1, Sebastian Zöllner, Gonçalo R Abecasis
1Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA. lianglim@umich.edu
Bioinformatics (Oxford, England)
|April 27, 2007
Summary
GENOME is a new tool for simulating whole genome data using a coalescent-based approach. It allows for variable recombination rates and flexible population histories, aiding in the study of genomic data.
Area of Science:
- Genomics
- Computational Biology
- Population Genetics
Background:
- Coalescent-based simulation is crucial for understanding genomic data.
- Existing simulators have limitations in handling complex genomic features.
Purpose of the Study:
- To introduce GENOME, a novel coalescent-based simulator for whole genome data.
- To enable flexible simulation of population histories and recombination rates.
Main Methods:
- GENOME utilizes a rapid coalescent-based simulation approach.
- It incorporates variable recombination rates along the genome.
- Flexible population histories can be modeled.
Main Results:
- Simulated data from GENOME exhibit expected Linkage Disequilibrium (LD) patterns and frequency spectra in small regions.
- The program's accuracy was verified against theoretical expectations.
Conclusions:
- GENOME provides a powerful tool for simulating whole genome data with realistic complexities.
- It facilitates the study of sampling properties for various statistics in large-scale genomic analyses.
- The software is publicly available for research use.
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