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Table 7 Comparison of different library preparation kits on FFPET using HiSeq 2500 Platform

From: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

Library preparation method Library preparation kit Input amount (ng) Duplicate read (%) Fragment size (stdev) Coveragea Ratio of bias in CpG island/shores
Pre-BS KAPA LTP (Kapa Biosystems) 1000 4.2 138 bp (41 bp) 5.4× 0.5:0.8
KAPA Hyperprep (Kapa Biosystems) 100 5.6 105 bp (49 bp) 3.9× 0.2:0.6
Post-BS TruSeq DNA methylation (Illumina) 50 9.6 73 bp (37 bp) 4.2× 3.3:2.0
TruMethyl WG v1.9 (Cambridge Epigenetix) 200 1.8 120 bp (49 bp) 5.1× 1.1:1.0
Accel-NGS methyl-seq (Swift Biosciences) 100 1.4 132 bp (50 bp) 6.6× 0.6:0.9
  1. aTwo lanes (HiSeq 2500 rapid run)