Comprehensive evaluation of new sequencer T20 and well-established T7 with 507 human samples

The DNBSEQ-T20x2 (T20) sequencer, developed by MGI Tech, enables cost-effective human whole-genome sequencing (WGS) at 30× coverage for less than $100 per genome. Here, we evaluate the sequencing performance and data quality of the T20 platform by benchmarking it against the established DNBSEQ-T7 (T7) sequencer using 507 samples derived from blood (N = 75), stool (N = 242), and saliva (N = 190). The T20 exhibited lower sequencing quality metrics compared with the T7, with Q20 scores of 95.76%-95.83% and Q30 scores of 87.25%-87.40%, compared with 97.81%-97.93% and 93.26%-93.60%, respectively, for T7 data. Quality differences were more evident toward the end of reads, and PCR-free libraries sequenced on the T20 showed similar reductions in quality scores. The median empirical base error rate estimated from 102 ZymoBIOMICS samples was 0.33%. The T20 demonstrated comparable coverage uniformity to the T7 and showed high concordance in microbiome composition analysis, with a median Bray-Curtis dissimilarity of 0.02. Variant calling performance was highly consistent between the two platforms. Among variants with non-missing genotype calls on both platforms, 94.92% of SNPs and 87.20% of indels showed concordant genotypes between T20 and T7. Overall, the T20 delivers reliable sequencing accuracy and reproducibility for large-scale genomic and microbiome studies, providing a cost-effective alternative for high-throughput sequencing applications.