Table 4. Summary of methods for whole genome bisulphite sequencing library preparation.

	TruSeq DNA methylation	SPLAT	Accel-NGS Methyl-Seq	NEBNextUltra
Input DNA quantity	50–100 ng	≤100 ng	≤100 ng	∼1000 ng
Number of PCR cycles	9	4 (100 ng input)	4 (100 ng input)	6
Amount of PCR duplicates	High	Low	Low	Low
Genome coverage	GC biased	Relatively uniform	Relatively uniform	AT biased
Advantages	Excellent coverage of CpG dense regions	High total CpG site coverage	High total CpG site coverage	_
	Methylation highly concordant with other methods	Methylation highly concordant with other methods	Methylation highly concordant with other methods
		Very low library prep cost
Disadvantages	High proportion of data removed in pre-processing steps	Coverage in CpG dense regions is lower than the average coverage	Coverage in CpG dense regions is lower than the average coverage	Overall low coverage of CpG sites, particularly in CpG dense regions
			Sequence tag removal is required