BSReadSim

BSReadSim is a versatile and efficient read simulator for genomic sequencing, supporting both conventional and bisulfite-based assays. It combines configurable biological and technical models to produce realistic reads with traceable ground truth. The resulting datasets can be used to guide experimental design, develop bioinformatics tools, and benchmark their performance 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}
}