Table 7 Running time of different methods for simulated reads with 8× coverage on chromosomes 21 and 22
From: SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
Method | Time (s) | Â | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | Minimap2 | NGMLR | Find reads in fastQ | Unify outputs | SAM to BAM | Sniffles | SVIM | Remove redundancy | Total | Speed-up |
Baseline method | 163 | – | – | – | 47 | 27 | – | – | 233 | 0.24 |
NGMLR-Sniffles | – | 1586 | – | – | 42 | 25 | – | – | 1653 | 1.68 |
Most sensitive method | 163 | 1586 | – | 16 | 50 | 29 | 35 | 2 | 1881 | 1.91 |
SVNN | 163 | 590 | 104 | 13 | 50 | 27 | 32 | 2 | 981 | 1 |