BSReadSim: a versatile and efficient simulator to generate realistic bisulfite sequencing reads

Realistic bisulfite sequencing simulators are crucial for advancing method development in computational epigenetics. However, existing tools often fall short due to oversimplified generative models that fail to capture the complexity of real data. We present BSReadSim, an efficient and versatile simulator that generatesrealistic bisulfite sequencing reads. BSReadSim excels in integrating reference genetic variants and methylation profiles, offering unmatched versatility across multiple sequencing technologies, including WGBS, RRBS, and TBS. By accurately modeling methylation patterns, sampling biases, sequencing errors, and leveraging optimized implementation, BSReadSim efficiently generates realistic synthetic datasets tailored to specific experimental needs while maintaining computational feasibility. By enhancing the realism and flexibility of bisulfite sequencing simulations, BSReadSim supports improved experiment design, method development, and benchmarking of computational tools, ultimately advancing the reliability and rigor of DNA methylation analysis tools.