Table 1. Comparison of read simulator features.

		ART	CuReSim	dwgsim	Gemsim	Mason	pIRS	SInC	NEAT
Mutation models	SNPs / indels		×	×	×		×	×	×
	Structural variation						*	×	*
	Any ploidy						*		×
	Learnable from data				*				×
	Accepts input variants			*	*				×
Sequencing models	Learn Q-score profile	×	*		×	*	×	×	×
	Learn error statistics	×	*		×	*	×	×	×
	GC% coverage bias		×		×		×		×
	Learn fragment lengths				*				×
Usability	Any read length	×	×	×	×		*	×	×
	Single & paired ended reads	×		×	×			×	×
	Any error rate	×	×	×			×		×
	Any mutation rate	×		×	×		×	×	×
	Targeted sequencing			×	×				*
Ground truth	Mapping positions	×	×	×		×			×
	CIGAR alignment	×				×			×
	Variant positions			×			×	*	×

Comparison of the main features of several existing read simulator packages.

×: feature is present in the simulator.

*: feature is either partially implemented or requires significant effort to fully use.