Other assays¶

Besides bisulfite sequencing, BSReadSim simulates whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing (TS).

Non-bisulfite workflow¶

The non-bisulfite workflow shares the genome, fragment, read, output, and seed controls without methylation modeling or bisulfite conversion.

reference FASTA
  -> prepared diploid genome
  -> fragment generation and sampling
  -> read extraction, base quality, and substitution errors
  -> FASTQ or annotated BAM + manifest

WGS: Samples fragments from eligible positions across the genome and requires no target file.
WES: Samples fragments around exome intervals supplied with --targets.
TS: Samples fragments around custom panel intervals supplied with --targets.

WES, TS, and TBS use the same target-centered fragment model.

Choose an assay¶

WGS¶

Use wgs for whole-genome sampling. This example uses the default uniform sampling.

bsreadsim run wgs \
  -r reference.fa \
  -o runs/wgs \
  -n 100000 \
  -t 4 \
  --mutation-rate 0 \
  --seed 42

See Generate fragments and Sample fragments for whole-genome fragment geometry and sampling controls.

WES¶

Use wes with exome intervals in a strand-aware BED6 file. This example uses the default uniform target sampling.

bsreadsim run wes \
  -r reference.fa \
  -o runs/wes \
  -n 100000 \
  -t 4 \
  --targets exome.bed \
  --insert-mean 300 \
  --center-sd 50 \
  --mutation-rate 0 \
  --seed 42

TS¶

Use ts with a custom target panel in a strand-aware BED6 file. This example weights targets by the scores in BED column 5.

bsreadsim run ts \
  -r reference.fa \
  -o runs/ts \
  -n 100000 \
  -t 4 \
  --sampling score \
  --targets panel.bed \
  --insert-mean 300 \
  --center-sd 50 \
  --mutation-rate 0 \
  --seed 42

Shared simulation controls¶

The following controls also apply to non-bisulfite assays:

Control	Use in non-bisulfite assays
Genome	Keep the reference unchanged, generate de novo variants, or load a diploid VCF
Fragment generation	Use whole-genome geometry for WGS and target-centered geometry for WES and TS
Fragment length	Set the minimum, mean, maximum, and standard deviation
Fragment sampling	Use `uniform` by default, `gc` for WGS, or `score` for WES and TS
Read count	Set an exact read count or assay-aware depth
Read layout	Choose single- or paired-end reads and set the read length
Quality and errors	Use fixed values or data-derived models for Phred scores and substitutions
Output and truth	Write FASTQ or annotated BAM, a manifest, and optional variant truth
Random seeds	Control genome preparation and fragment and read generation; the methylation seed is unused

How depth is calculated

WGS depth uses the full length of every contig with positive fragment- allocation weight. WES and TS depth use the union of all validated target intervals, including intervals whose individual geometry or score prevents selection. Use --reads instead when an exact output record count is required.

Outputs and simulation truth¶

Each run writes FASTQ or an origin-annotated BAM, together with a manifest. With the default prefix sim, a paired-end FASTQ run using --save-truth has the following structure:

OUTPUT/
├── sim.R1.fastq.gz
├── sim.R2.fastq.gz
├── sim.manifest.json
└── truth/
    └── sim.variants.vcf.gz

Single-end FASTQ omits sim.R2.fastq.gz. BAM output replaces the FASTQ files with sim.bam and omits bisulfite-specific XG, XR, and YS annotations. The required generic zt and zr fields remain present but contain no methylation or conversion events. For non-bisulfite assays, --save-truth exports only the prepared, phased variant set as VCF.

See Configure output, Save simulation truth, and Outputs for the available representations, artifact names, and completion rules.