Table 8 Running time of different methods for simulated reads with 12× coverage on chromosomes 21 and 22
From: SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
| Â | Time (s) | Â | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Method | Minimap2 | NGMLR | Find reads in fastQ | Unify outputs | SAM to BAM | Sniffles | SVIM | Remove redundancy | Total | Speed-up |
Baseline method | 281 | – | – | – | 78 | 72 | – | – | 431 | 0.28 |
NGMLR-Sniffles | – | 2687 | – | – | 66 | 67 | – | – | 2820 | 1.84 |
Most sensitive method | 281 | 2687 | – | 51 | 119 | 77 | 51 | 2 | 3266 | 2.14 |
SVNN | 281 | 766 | 196 | 43 | 117 | 74 | 50 | 2 | 1529 | 1 |