Table 1 Average execution time comparison of the tools for the six benchmarks
From: JOA: Joint Overlap Analysis of multiple genomic interval sets
Benchmarks | Average execution times in seconds | ||||||
|---|---|---|---|---|---|---|---|
(1n,1ppn) | (1n,8ppn) | ||||||
GROK | BEDOPS | BEDTools | JOA ST | JOA ISTF | JOA ST | JOA ISTF | |
2 small files | 1.1426 | 0.1785 | 0.4204 | 1.5135 | 1.7880 | 0.8363 | 0.9712 |
5 small files | 2.3757 | 0.3104 | 12.6509 | 2.1504 | 2.7396 | 1.2470 | 1.5531 |
(2.3M, 2.3M) | 13.5173 | 1.8656 | 14.4679 | 16.1611 | 17.0239 | 9.5708 | 9.7355 |
(6.4M, 6.4M) | 34.2736 | 4.8053 | 63.8499 | 39.7799 | 43.5383 | 23.9280 | 24.0116 |
(9.2M, 9.2M) | 54.5452 | 7.1102 | 65.3324 | 56.0001 | 55.9838 | 31.7290 | 32.5613 |
(6.4M, 9.2M) | 49.2007 | 5.4660 | 43.1104 | 48.0046 | 47.9815 | 23.2048 | 24.3927 |