Table 1.
Breakdown of times of principal steps for rapid diagnostic whole genome sequencing
| Method | Sample | Site | DNA isolation, QC and shearing | PCR-free library prep | WGS library QC | SBS | Yield (GB) | % > Q30 | Alignment | Variant calling | RUNES variant annotation | Provisional diagnosis | Total time |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Published WGS50 | Multiplea | Both | 2:30 | 3:15 | 1:30 | 25:30 | 139 | 90 | 14:40 | 2:30 | 0:05 | 50:00 | |
| SBS18, GSNAP/GATK/noVQSR | 5006-01 | CMH | 2:30 | 3:15 | 1:30 | 19:45 | 128 | 91 | 22:30 | 0:29 | n.a. | 49:59 | |
| WGS26, SBS18, and Dragen v1.2 | UDT_173 | Essex | 2:30 | 3:02 | 1:30 | 17:58 | 106 | 92 | 0:15 | 0:15 | 0:34 | 0:04 | 26:08 |
| WGS26, SBS18, and Dragen v1.2 | UDT_103 | Essex | 2:30 | 3:05 | 1:30 | 18:25 | 130 | 90 | 0:19 | 0:22 | 0:31 | 0:05 | 26:47 |
| WGS26, SBS18, and Dragen v1.2 | NA12878 | Essex | 2:30 | 3:15 | 1:30 | 18:00 | 143 | 85b | 0:19 | 0:22 | 0:33 | n.a. | 26:28 |
| WGS26, SBS18, and Dragen v1.2 | NA12878 | CMH | 2:30 | 3:15 | 1:30 | 18:36 | 65c | 85b | 0:10 | 0:11 | 0:35 | n.a. | 26:47 |
GB, gigabases; Q, Phred-like quality score QC, quality control; SBS, 2 × 101 cycle sequencing-by-synthesis
aReference 12
bPrior to SBS18, after failing tiles were removed
cSingle flowcell