Table 10 Running time of different methods for real 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 | 838 | – | – | – | 82 | 41 | – | – | 961 | 0.27 |
NGMLR-Sniffles | – | 3577 | – | – | 86 | 60 | – | – | 3723 | 1.04 |
Most sensitive method | 838 | 3577 | – | 91 | 142 | 98 | 85 | 10 | 4841 | 1.35 |
SVNN | 838 | 1780 | 561 | 87 | 132 | 96 | 81 | 9 | 3584 | 1 |