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Table 4 Running time (in seconds) of nanoGapFiller for filling the gaps of 12 species

From: Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Species

#Contigs in assembly graph

#Sites in site graph

#Edges in site graph

#Filled gaps

Total length of gaps (nt)

Running time (s)

S. ynec

250

774

1905

11

181,832

5.24

S. coelicolor

926

3,532

8160

17

478,321

25.95

S. agal

204

546

5554

16

463,622

8.04

P. syringae

1492

2176

51,343

25

732,210

371.05

P. putida

752

2190

15,759

9

2856,292

188.39

N. farcinica

388

924

2192

19

639,552

10.15

E. coli

734

1348

40,858

23

922,021

88.08

E. carotovora

622

1454

2636

19

586,169

9.42

C. hutchinsonii

596

990

5105

25

895,179

12.24

B. pseudomallei

390

2144

2662

8

175,737

3.83

B. japonicum

992

3524

26,014

29

1021,611

1721.27

A. vari

870

474

135,667

17

4917,178

71,067.07

  1. Here, the gaps are identified using simulated optical maps with alignment method SOMA2. CPU: AMD Opteron 6344; OS: Ubuntu 16.04; Python version: 3.6.7