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Table 1 Comparison of different library preparation kits on intact genomic DNA 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) Size selection (bp) Duplicate read (%) Fragment size (stdev) Coverageb Ratio of bias in CpG island/shores
Pre-BS KAPA LTP (Kapa Biosystems) 1000 < 300a 1.00 175 bp (42 bp) 8.8× 0.7:0.9
> 300 3.50 226 bp (69 bp) 12.4× 0.3:0.7
< 400 0.72 229 bp (62 bp) 13.5× 0.3:0.6
> 400 1.90 237 bp (82 bp) 17.2× 0.8:0.9
KAPA Hyperprep (Kapa Biosystems) 100 < 300a 5.50 164 bp (72 bp) 6.3× 0.3:0.7
> 300 5.50 189 bp (88 bp) 7.0× 0.3:0.7
Post-BS TruSeq DNA methylation (Illumina) 50 < 200a 10.00 156 bp (77 bp) 4.0× 2.1:1.5
TruMethyl WGv 1.9 (Cambridge Epigenetix) 200 > 300a 0.95 227 bp (98 bp) 12.9× 0.8:1.1
Accel-NGS Methyl-Seq (Swift Biosciences) 100 < 300a 1.40 179 bp (61 bp) 10.7× 0.7:0.9
  > 300 1.10 202 bp (70 bp) 12.6× 0.7:0.9
  1. aManufacturer’s recommended method
  2. bTwo lanes( HiSeq 2500 rapid run)