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