Table 2.
Comparison of R9 and R10 sequencing of the HG002 cell line.
| Benchmark | HG002 R9 | HG002 R10 kit V14 |
|---|---|---|
|
| ||
| Assembly benchmarks | ||
|
| ||
| Asm. size | 2.896 Gb | 2.927 Gb |
| Asm. NG50 | 21.4 Mb | 14.9 Mb |
| Asm. phase block N50 | 1.010 Mb | 0.99 Mb |
| Asm. SNP switch | 0.00165 | 0.0015 |
| Asm. QV | 34.3 | 42.8 |
| Asm. SNP recall / precision | 0.9795/0.9528 | 0.9851 / 0.9856 |
|
| ||
| Small variant calls benchmarks (recall / precision) | ||
|
| ||
| SNP (GIAB Tier 1) | 0.997 / 0.9982 | 0.9979 / 0.998 |
| Indel (GIAB Tier 1) | 0.7217 / 0.8715 | 0.8495 / 0.8991 |
| Indel (no homopol. or tandem repeats) | 0.9609 / 0.9807 | 0.9970 / 0.9969 |
| Indel (RefSeq CDS) | 0.9121 / 0.9342 | 0.9948 / 0.9748 |
|
| ||
| Structural variant benchmarks (recall / precision) | ||
|
| ||
| SV (GIAB Tier1) | 0.9782 / 0.9557 | 0.975 / 0.9595 |
| SV (HPRC non-Cen non-SD) | 0.9689 / 0.9685 | 0.9764 / 0.9835 |
| SV (HPRC only SD) | 0.4921 / 0.6064 | 0.5277 / 0.6355 |
Substantial improvements in different categories are highlighted in bold. Benchmarks were performed using the methods described above in the manuscript.