pWGBSSimla

pWGBSSimla simulates whole-genome bisulfite sequencing (BS-seq) data by incorporating methylation quantitative trait loci (meQTLs), allele-specific methylations (ASM), and differentially methylated regions (DMRs) to generate realistic datasets for benchmarking methylation analysis methods.

Key Features:

• Profile-Based Simulation: Simulates bisulfite sequencing data across experimental designs including WGBS, RRBS, and oxBS-seq.
• Incorporation of meQTLs: Models the impact of genetic variants on methylation levels using block structures of CpG site methylation status.
• ASM Modeling: Captures allele-specific methylations to represent allele-dependent methylation patterns.
• DMR Simulation: Generates differentially methylated regions based on observed methylation rate distributions from real data to reflect cell-type-specific differences.

Scientific Applications:

• Methylation Analysis Method Validation: Facilitates performance comparisons among methylation analysis methods by generating realistic BS-seq datasets for method development and validation studies.

Methodology:

The simulator models meQTLs and ASM using CpG methylation-status block structures and simulates DMRs using observed methylation rates from real-world data.