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Quick start

1. Prepare a reference genome

Obtain a reference genome in FASTA format. This demo uses the repository's bundled test.fa. For real analyses, prepare or download a reference genome from Ensembl or GENCODE that matches the species and build in your study.

2. Run a WGBS simulation

bsreadsim run wgbs \
  -r test.fa \
  -o test/ \
  -n 1000 \
  -t 4 \
  --seed 42
Command options

run wgbs simulates WGBS reads. In this command:

  • -r specifies the reference FASTA;
  • -o specifies the output directory;
  • -n specifies the total number of reads to generate (n/2 read pairs);
  • -t sets the number of threads;
  • --seed specifies the master seed;

All other parameters use the WGBS defaults. See Customize for more configuration options.

3. Inspect the output

This command uses the default paired-end mode and fastq.gz format, so the output directory contains two FASTQ files and a run manifest:

test/
├── sim.R1.fastq.gz
├── sim.R2.fastq.gz
└── sim.manifest.json

Preview the first R1 record:

zcat test/sim.R1.fastq.gz | head -n 4

The manifest records the effective configuration, provenance, and run summary:

head -n 40 test/sim.manifest.json

Continue with customized simulation

Choose WGBS, RRBS, TBS, or a non-bisulfite assay. Then check the following