Table 1. Time and memory consumption.

Tools	Time (h:m)	Peak Memory Usage (GB)
CONGA	0:09	1.2
GenomeSTRiP	1:22	2.2
FREEC	0:39	7.1
CNVnator	0:32	14.1

Time and memory consumption of each algorithm for a simulated genome of 5× depth of coverage with 1680 deletions and 1684 duplications. “Time” refers to wall clock time and “Peak memory usage” is the maximum resident set size. Note that GenomeSTRiP has two steps in its pipeline: preprocessing and genotyping. Here, time was calculated by summing the running times of each step, and memory by taking the maximum. For CONGA, we used default parameters used in the simulation experiments.