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Table 9 Running time of different methods for simulated reads with 12× coverage on chromosome 1

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

 

Time (s)

 

Method

Minimap2

NGMLR

Find reads in fastQ

Unify outputs

SAM to BAM

Sniffles

SVIM

Remove redundancy

Total

Speed-up

Baseline method

556

–

–

–

203

130

–

–

889

0.48

NGMLR-Sniffles

–

5446

–

–

202

123

–

–

5771

3.14

Most sensitive method

556

5446

–

105

346

142

147

1

6743

3.66

SVNN

556

278

439

97

205

128

134

1

1838

1