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Table 2 Library preparation parameters of WGBS strategies compared in this study

From: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Method Strategy BS conversion PCR cycles Polymerase Libraries/Studies/Labs
Alkaline Pre-bisulfite Alkaline 15–18 Pfu Turbo Cx 18/2/1
Heat Pre-bisulfite Heat 10–16 Pfu Turbo Cx 49/4/3a
KAPA Pre-bisulfite Heat and alkaline 6–15 KAPA Uracil+ 47/4/2
Am-BS Pre-bisulfite Am-BS 9 JumpStart 14/2/1
PBAT Post-bisulfite Heat Noneb – 51/3/2
ampPBAT Post-bisulfite Heat and alkalinec 5–12b KAPA HiFi 23/4/2
EpiGnome Post-bisulfite Heat 9–10b FailSafe 14/2/2
  1. aOne of the ‘Heat’ studies is generated with Hot Start Taq and is only used as part of Set 2 for Fig. 5 and Additional file 2: Figure S6 and S7
  2. bInclude one, three or five steps of strand synthesis and pre-PCR enrichment (see Additional file 1)
  3. cThe alkaline procedure has modifications from the manufacturer’s protocol (see Additional file 1)
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