Table 2. Benchmarking metrics.

Each of the three runs for each tool is shown in this table. All values are taken directly from slurm’s sacct and seff features. All metrics are intuitive except for CPU efficiency, which is a measure of idle CPUs to CPU time over wall clock time.

Platform	Tool	Wall clock time (D-H:M:S)	CPU time (D-H:M:S)	CPU efficiency	Memory utilized (Gb)
Nanopore	Graphmap2	14-00:00:04	560-00:02:40	65.25%	90.19
		14-00:00:17	560-00:11:20	63.34%	94.58
		14-00:00:15	560-00:10:00	64.23%	89.68
	Minimap2	1-11:00:08	58-08:05:20	7.51%	12.43
		1-10:48:18	58-00:12:00	7.51%	12.80
		1-11:07:00	58-12:40:00	7.51%	12.78
	NGMLR	10-00:00:03	400-00:02:00	97.70%	35.86
		10-00:00:10	400-00:06:40	99.56%	34.38
		9-14:55:56	384-21:17:20	93.43%	36.34
	Winnowmap2	15:25:58	25-17:18:40	83.82%	29.48
		15:19:14	25-12:49:20	83.61%	30.02
		15:15:24	25-10:16:00	83.06%	28.74
SMRT-CCS	Graphmap2	5-01:33:22	202-14:14:40	98.88%	45.07
		5-02:54:53	204-20:35:20	98.81%	44.90
		5-06:49:25	211-08:56:40	98.52%	48.96
	LRA	6:53:00	11-11:20:00	33.20%	20.63
		6:53:04	11-11:22:40	33.11%	21.10
		6:32:33	10-21:42:00	33.22%	27.91
	Minimap2	11:02:04	18-09:22:40	7.51%	9.10
		11:06:03	18-12:02:00	7.51%	9.13
		10:55:09	18-04:46:00	7.52%	9.09
	NGMLR	21:50:29	36-09:39:20	99.20%	25.53
		22:24:38	37-08:25:20	99.19%	25.69
		21:58:53	36-15:15:20	99.53%	25.82
	Winnowmap2	3:39:42	6-02:28:00	88.10%	18.57
		3:43:42	6-05:08:00	88.32%	18.71
		3:40:32	6-03:01:20	87.91%	19.14