BSReadSim

BSReadSim efficiently simulates reads for conventional genomic sequencing as well as bisulfite-based assays. Its configurable models capture biological variation alongside technical effects, producing realistic reads with traceable ground truth. The resulting datasets support experimental design, bioinformatics tool development, and performance benchmarking under controlled conditions. Learn more in the BSReadSim preprint.

Quick start Workflow

Supported assays

WGBS

Whole-genome bisulfite sequencing profiles DNA methylation at single-base resolution across the genome.

Configure WGBS

RRBS

Reduced representation bisulfite sequencing enriches CpG-rich regions through restriction-enzyme digestion and size selection.

Configure RRBS

TBS

Targeted bisulfite sequencing enriches predefined genomic regions through probe-based capture.

Configure TBS

Other assays

Additional support includes conventional whole-genome, whole-exome, and targeted sequencing.

Learn more

Installation

Install the current release on Linux or WSL2.

Installation guide

Customization

Tailor models and parameters to your study in Customize. For complete commands organized by simulation goal, see Tutorials.

Customize View tutorials

Output

Each run produces reads as FASTQ files or an origin-annotated BAM, together with a manifest. The underlying variant set and methylation profile can optionally be saved as VCF and MethDB files for reuse.

Explore outputs View file formats

Citation

If you use BSReadSim in your research, please cite the BSReadSim preprint:

@article{guo2024bsreadsim,
  title = {BSReadSim: a versatile and efficient simulator to generate realistic bisulfite sequencing reads},
  author = {Guo, Wenbin and Pellegrini, Matteo},
  journal = {bioRxiv},
  year = {2024},
  publisher = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2024.12.24.627620}
}