Table 1 Sequencing summary from multiple NGS technologies. Whole-genome and transcriptome sequencing data from multiple NGS platform for structural variants (SVs) and fusion gene detection in HCC1395 and HCC1395BL reference samples
NGS Technologies | Materials | Library protocols | Average library insert sizes | Total number of reads (genome coverage) | |
|---|---|---|---|---|---|
HCC1395 | HCC1395BL | ||||
Illumina WGS on HiSeq/NovaSeq/X10 | Fresh DNA | Illumina TruSeq DNA PCR Free 1μg Input Library Prep | 400bp | 35 billion (1,148X) | 34 billion (1,119X) |
Fresh DNA with mixture of tumor and normal cells for purity study | Illumina TruSeq DNA PCR Free 1μg Input Library Prep | 400bp | 64 billion (2348X) | ||
10X Genomics WGS | Fresh DNA | 10X Genomics Chromium Genome V2 kit | 65kb | 23 billion (974X) | 21 billion (881X) |
PacBio WGS on Sequel | Fresh DNA | PacBio Sequel 10 kb Library Prep with Sequel Chemistry Kits v 2.1 | 10kb | 116 million (39X) | 132 million (44X) |
Hi-C WGS on NextSeq | Fresh DNA | Dovetail SELVA Library Prep Kit | NA | 200 million (34X) | 200 million (34X) |
Oxford Nanopore | Fresh DNA | Oxford Nanopore SQK-LSK109 ligation sequencing kit | 9kb | 8 million (12X) | 20 million (19X) |
Illumina RNA-seq on NextSeq | Fresh RNA | NuGEN Ovation RNA-seq Library Prep | 300bp | 188 million | 192 million |