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DNemulator

DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion.

• Simulate polymorphisms based on real polymorphisms and their frequencies
• Simulate diploid genomes
• Simulate sequencing errors based on real per-sequence, per-base error probabilities
• Simulate various cytosine methylation rates depending on cg-context, and bisulfite conversion

Get the latest version: dnemulator-16.zip

The bisulfite alignment benchmark provides an example of using DNemulator.

Related

Sherman can also simulate bisulfite sequencing experiments. DNemulator can do some things that Sherman cannot, and vice-versa.

MethylCoder includes a BS-Seq Benchmark, using real (not simulated) data. This is obviously more realistic, but it has the disadvantage that the ground truth is unknown.