Performance evaluation of structural variation detection using DNBSEQ whole-genome sequencing

DNBSEQ platforms have been widely used for variation detection, including single-nucleotide variants (SNVs) and short insertions and deletions (INDELs), which is comparable to Illumina. However, the performance and even characteristics of structural variations (SVs) detection using DNBSEQ platforms are still unclear. In this study, we assessed the detection of SVs using 40 tools on eight DNBSEQ whole-genome sequencing (WGS) datasets and two Illumina WGS datasets of NA12878. Our findings confirmed that the performance of SVs detection using the same tool on DNBSEQ and Illumina datasets was highly consistent, with correlations greater than 0.80 on metrics of number, size, precision and sensitivity, respectively. Furthermore, we constructed a “DNBSEQ” SV set (4,785 SVs) from the DNBSEQ datasets and an “Illumina” SV set (6,797 SVs) from the Illumina datasets. We found that these two SV sets were highly consistent of SV sites and genomic characteristics, including repetitive regions, GC distribution, difficult-to-sequence regions, and gene features, indicating the robustness of our comparative analysis and highlights the value of both platforms in understanding the genomic context of SVs. Our study systematically analyzed and characterized germline SVs detected on WGS datasets sequenced from DNBSEQ platforms, providing a benchmark resource for further studies of SVs using DNBSEQ platforms.