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Table 2 Number of interval files are increased by two fold whereas number of intervals in each file is kept constant

From: JOA: Joint Overlap Analysis of multiple genomic interval sets

Simulations 1st Scenario (#ofFiles,#ofIntervals)

Average execution times in seconds

 

(1n,1ppn)

(1n,2ppn)

 

GROK

BEDOPS

BEDTools

JOA ST

JOA ISTF

JOA ST

JOA ISTF

(2,100000)

0.6973

0.0366

0.2380

1.0846

1.2861

0.6677

0.7121

(4,100000)

1.3527

0.0397

3.8666

1.4480

1.7342

1.0410

1.0932

(8,100000)

2.7232

0.0447

8.2620

2.0175

2.4720

1.4686

1.5197

(16,100000)

5.7325

0.0565

18.9487

2.8402

3.6387

2.0252

2.3860

(32,100000)

12.5799

0.0819

45.7564

4.4840

5.4132

3.0647

3.6630

(64,100000)

30.2584

0.1283

116.7736

6.9214

7.9966

4.5746

5.4844

(128,100000)

66.7122

0.2131

312.8438

12.1682

13.6740

7.4285

8.3240

(256,100000)

-

0.4229

891.2454

22.6010

24.0628

15.3915

16.2595

(512,100000)

-

0.8283

2887.3816

42.0187

45.3321

26.9868

28.8161

  1. Average execution time comparison of the tools for the first scenario using semi-synthetic datasets. GROK, JOA, BEDTools and BEDOPS execution times are averaged over 50 runs except BEDTools runs for 128, 256 and 512 files which are averaged over 2 runs