Markup | Genome Research

Table 1.

Runtime (min) of each tool on Chr 1 of the HG002 genome for ONT, PacBio, and Illumina reads

	ONT				PacBio				Illumina
Tool	5×	10×	15×	30×	5×	10×	15×	30×	5×	10×	15×	30×
HapCUT2	0.93	1.83	2.66	4.97	0.75	1.44	1.96	4.65	0.24	0.51	0.70	1.55
LongPhase	0.23	0.41	0.65	1.36	0.28	0.36	0.66	1.20	—	—	—	—
RefHap	0.58	1.61	6.22	92.98	1.03	2.69	8.36	167.63	0.71	0.96	1.24	3.87
WhatsHap	0.69	2.78	6.51	11.32	0.64	2.44	12.09	12.77	1.41	3.27	7.88	13.86
Ralphi	1.13	2.83	5.27	15.43	0.97	1.66	2.73	12.58	1.86	3.18	4.39	7.18
Memory (GB)	1.40	1.99	3.54	11.50	1.40	1.61	2.57	12.22	1.20	1.79	2.38	4.22

[i] Memory usage is reported for Ralphi. Runtime is an average over three separate runs.