Comparison of PCR-free libraries

To enable comparision between NEBNext Ultra II, NEBNext Ultra II FS, and Illumina DNA PCR-Free library prep methods, sequencing libraries were prepared according the manufacturer recommendations from 250 ng of NA19240 cell line DNA and sequenced on a single NovaSeq 6000 S4 v1.5 flowcell (PE 2x150 bp). Reads were adapter trimmed (fastp 0.20.0), aligned) to the Telomere-to-Telomere chm13 reference (draft 1, bwa-mem 0.7.17), and duplicate marked (samblaster 0.1.24). 2.8B reads were randomly sampled from each bam (sambamba view -s 0.6.8).

为对比NEBNext Ultra II、NEBNext Ultra II FS与Illumina DNA PCR-Free（Polymerase Chain Reaction-Free，聚合酶链式反应无扩增）建库方法的性能差异，本研究依照各厂商推荐方案，以250纳克NA19240细胞系基因组DNA构建测序文库，随后在单张NovaSeq 6000 S4 v1.5流动槽上完成PE（Pair-End，双端）2×150 bp测序。测序读段先经fastp 0.20.0完成接头修剪，再通过bwa-mem 0.7.17比对至端粒到端粒的chm13参考基因组（草稿版1），并使用samblaster 0.1.24标记PCR重复序列。最后通过sambamba 0.6.8执行view命令，从每个BAM（Binary Alignment Map，二进制比对映射）文件中随机抽取28亿条读段。