RRBSsim

Key Features:

• RRBS Data Simulation: Generates bisulfite-converted sequencing reads that replicate CpG methylation patterns and sequencing depth characteristics of RRBS experiments.
• Aligner Performance Benchmarking: Evaluates mapping accuracy at CpG sites, including CpG island (CGI) shores and gene bodies, assessing recall and precision across varying methylation levels.

Scientific Applications:

• Genome-Wide DNA Methylation Analysis: Supports evaluation and optimization of bisulfite read aligners such as bwa-meth and BS-Seeker2 (bowtie2) for single-base resolution methylation studies.

Methodology:

RRBSsim models bisulfite conversion by converting unmethylated cytosines and simulates RRBS reads across reference genomes, enabling empirical assessment of CpG methylation detection and alignment performance in challenging genomic regions.