Workflow¶

BSReadSim generates sequencing reads through a workflow that mirrors the key biological and technical stages of an experiment. It first prepares a diploid genome, then applies assay-specific fragment sampling. Bisulfite modes additionally construct site-specific methylation probabilities, draw methylation states, and apply bisulfite conversion. Finally, it adds base qualities and sequencing errors before exporting reads as FASTQ or origin-annotated BAM.

From reference genome to sequencing reads¶

BSReadSim workflow from a reference genome through variants, haplotypes, optional methylation and bisulfite conversion, assay-specific sampling, sequencing errors and read output — BSReadSim resolves the genome and methylome before sampling physical fragments, generating reads, and writing FASTQ or origin-annotated BAM with a run manifest.

Five stages of read simulation¶

Stage	Description
Genome	Resolve two haplotypes from the reference genome, optionally incorporating VCF variants or de novo mutations.
Methylome	For bisulfite modes, prepare methylation probabilities using beta distributions and any provided measured or allele-specific profiles.
Fragmentation	Generate physical DNA fragments across whole-genome, restriction-fragment, or targeted domains using uniform or profile-based sampling.
Sequencing	Sequence fragments according to the selected assay protocol, then assign base qualities and introduce sequencing errors.
Output	Output reads as FASTQ or annotated BAM, with a provenance manifest.

The order matters because variants can change cytosine contexts, methylatable sites, RRBS cut sites, and fragment opportunities. Each upstream layer is therefore resolved before the next one.

Six supported sequencing assays¶

BSReadSim supports three bisulfite assays (WGBS, RRBS, and TBS) and three non-bisulfite assays (WGS, WES, and TS), spanning whole-genome and region-enrichment protocols. The figure below summarizes the experimental strategies used in the three bisulfite assays.

Comparison of WGBS genome-wide sampling, RRBS restriction-enzyme digestion, and TBS BED-targeted sampling — WGBS uses random fragmentation for genome-wide coverage; RRBS enriches CpG-rich regions through restriction-enzyme digestion and size selection; and TBS enriches predefined targets through probe enrichment.

See Tutorials for runnable examples, Customize for model options, and Other assays for non-bisulfite workflows.