Table 1.

Performance of interval operations

Operation	Bedtk	BEDTools	BEDOPS
Sort	5.35 s/393 MB	21.14 s/2731 MB	11.25 s/205 MB
Intersect	6.42 s/19 MB	54.87 s/397 MB	8.78 s/3 MB
Coverage	10.91 s/19 MB	257.11 s/678 MB

Note: Each cell gives the CPU time in sections and peak memory in megabases (MB) measured on a Linux server with two AMD EPYC 7301 CPUs at 2.2 GHz. The ‘sort’ operation sorts file 2. ‘intersect’ reports intervals in file 2 that overlaps intervals in file 1. For each interval in file 2, ‘coverage’ computes the number of bases covered by intervals in file 1. BEDOPS does not support the ‘coverage’ operation. It also requires sorted input for ‘intersect’; sorting time is excluded. All operations are CPU bounded, not I/O bounded.