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Table 6 Running time of different methods for simulated reads with 10× coverage on chromosomes 21 and 22

From: SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

Method

Time (s)

 
 

Minimap2

NGMLR

Find reads in fastQ

Unify outputs

SAM to BAM

Sniffles

SVIM

Remove redundancy

Total

Speed-up

Baseline method

204

–

–

–

61

37

–

–

302

0.25

NGMLR-Sniffles

–

1961

–

–

50

34

–

–

2045

1.74

Most sensitive method

204

1961

–

28

65

37

43

2

2340

1.98

SVNN

204

665

146

21

64

37

40

2

1179

1