DNBSEQ-T1+ vs NovaSeq X Plus:
Third-Party Benchmark
Key Takeaways
Summary
- •Base Accuracy Sets a New Benchmark: At PE150 in WGS, T1+ delivers a Q30 of 98% versus 88% for NovaSeq X Plus, and sustains a Q40 of 94% versus 88% — a 10-point lead at Q30 and a 6-point lead at the far stricter Q40 threshold.
- •Higher Effective Data Utilization: In WES, T1+ records a PCR duplicate rate of just 1.685% versus 7.289% for NovaSeq X Plus — less than one quarter — converting more of every gigabyte into usable depth and lowering the effective cost per sample.
- •Comparable Target Capture and Coverage Uniformity: On Twist EF2.0 + Exome 2.0 libraries, T1+ delivers an on-target rate of 89.8% versus 89.6%, mean coverage depth of 121.2× versus 120.4×, and a Fold-80 base penalty of 1.40 versus 1.39 — on par with NovaSeq X Plus across all three metrics.
Overview
A research team at a leading Japanese university recently benchmarked several high-throughput sequencing platforms in parallel on real research samples. This article reports the head-to-head results for MGI’s DNBSEQ-T1+ (T1+) and NovaSeq X Plus.
Using a standardized workflow, the team compared the two platforms on base accuracy in whole-genome sequencing (WGS), and on duplicate rate, target capture and coverage uniformity in whole-exome sequencing (WES). T1+ showed higher base accuracy in WGS and a much lower duplicate rate in WES, with target capture and coverage uniformity on par with NovaSeq X Plus.
Application 1: Whole-Genome Sequencing (WGS)
Human whole-genome samples were sequenced at PE150 on both platforms and compared on base quality.
Result: Higher Base Accuracy
T1+ achieved a Q30 of 98% versus 88% for NovaSeq X Plus, and a Q40 of 94% versus 88%. Bases at Q30 or above have a base-calling accuracy of at least 99.9%, and bases at Q40 or above at least 99.99%. A larger share of bases clearing both thresholds gives variant detection and genome assembly a more reliable starting point.
Figure 1 shows mean base quality across the 150 cycles of each read. T1+ holds a flat, high quality profile for both reads, while NovaSeq X Plus varies more across the run, particularly in read 2.
Table 1. Base quality and GC content (WGS, PE150)
| Metric | NovaSeq X Plus | DNBSEQ-T1+ |
|---|---|---|
| > Q30 | 88% | 98% |
| > Q30 (catalog) | 85% | 93% |
| > Q40 | 88% | 94% |
| %GC | 43.8% | 41.2% |
Application 2: Whole-Exome Sequencing (WES)
| Sequencer | Reads | %duplicate | %ontarget | meancoverage | Fold 80 |
|---|---|---|---|---|---|
| NovaSeq X Plus | 29,864,479 | 0.07289 | 0.896 | 120.4 | 1.39 |
| DNBSEQ-T1+ | 29,932,145 | 0.01685 | 0.898 | 121.2 | 1.40 |
Results
A.T1+ Cuts the PCR Duplicate Rate to One-Quarter of NovaSeq X Plus
T1+ recorded a duplicate rate of 1.685% versus 7.289% for NovaSeq X Plus. Duplicate reads add no new information, so the higher the rate, the more sequencing output is wasted.
DNBSEQ™ rolling circle amplification avoids the accumulation of errors and duplicates associated with exponential amplification. At equal data volume, T1+ therefore yields more usable depth, making better use of every gigabyte sequenced and limiting amplification bias in variant calling.
B.T1+ Matches NovaSeq X Plus on Target Capture, Coverage Depth and Uniformity
T1+ delivers an on-target rate of 89.8%, on par with the 89.6% of NovaSeq X Plus and among the best in the industry — confirming the platform’s compatibility with exome capture libraries and its consistency in targeted sequencing.
At equal data volume, T1+ reaches an average coverage depth of 121.2× versus 120.4×, with a Fold-80 base penalty of 1.40 versus 1.39 — matching NovaSeq X Plus on both depth and uniformity.
Uniform coverage is what allows the whole exome to be interrogated. T1+ sustains that uniformity at high depth, reducing the risk of missed variants in low-coverage regions and keeping exome detection accurate.
Conclusion
This third-party evaluation examined T1+ from base quality through to application performance, across WGS and WES:
- WGS: T1+ delivered higher base accuracy than NovaSeq X Plus, with 98% of bases at Q30 or above and 94% at Q40 or above, versus 88% for both thresholds.
- WES: T1+ converted more of its raw output into usable data, with a duplicate rate under a quarter of NovaSeq X Plus and on-par coverage performance.
As the world’s first desktop sequencer to generate terabase-scale data within 24 hours, T1+ combines high throughput, high accuracy, high flexibility and high speed. It brings terabase-scale production within reach of more laboratories, without the space footprint of a conventional high-throughput facility.
As DNBSEQ technology continues to advance, MGI’s platforms are earning the trust of a growing number of research and clinical institutions worldwide. MGI will keep pushing sequencing innovation forward, giving users more efficient, accurate and accessible tools to advance life science research and precision medicine.
