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Table 3 Summary of biases affecting the pre- and post-BS WGBS library preparation strategies

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

Bias Main result figures Pre-bisulfite Post-bisulfite
GC-biasing AT-biasing (KAPA) Amplification-free With amplification
Degradation bias (C depletion) Figs. 1a and 2a, c +++ +++ + +
PCR (polymerase) bias Figs. 2a–c and 5f +++ + + +++
Modified C bias Figs. 1d and 3d ++ ++ + ++
Conversion artefacts Fig. 4 ++ + + +
Global 5mC overestimation Fig. 2d +++ ++ + ++
  1. For simplicity, pre-BS methods have been divided into GC-biasing (Heat, Alkaline and Am-BS) and AT-biasing (KAPA), and post-BS methods into amplification-free (PBAT) and with amplification (ampPBAT and EpiGnome). A plus sign indicates low bias, two plus signs medium bias and three high bias