Table 2.

Summary of the software comparison between varVAMP, Olivar and PrimalScheme

		SARS-CoV-2	BoDV-1	HAV	HEV cluster 2	HEV cluster 4	PV	ratHEV
varVAMP	Running time	1 min 9 s	16 s	12 s	22 s	10 s	11 s	9 s
	Number of amplicons	55	27	7	7	6	7	6
	% alignment coverage	100	99	96	99	99	100	97
	Mean mismatches per primer	0.002	0.17	0.15	0.21	0.20	0.13	0.43
Olivar	Running time	14 min 54 s	2 min 55 s	38 s	37 s	39 s	52 s	28 s
	Number of amplicons	61	28	5	7	8	10	5
	% alignment coverage	99	95	79	94	92	99	81
	Mean mismatches per primer	0.001	0.44	0.88	1.03	1.09	1.63	2.11
Primalscheme (alignment)	Running time	7 min 32 s	23 min 52 s	17 h 11 min 33 s	8 h 8 min 4 s	50 h 25 min 56 s	5 h 37 min 56 s	48 s
	Number of amplicons	49	25	6	8	8	8	6
	% alignment coverage	100	88	79	99	97	95	91
	Mean mismatches per primer	0.027	0.29	0.78	1.04	1.19	1.65	4.17
Primalscheme (consensus)	Running time	8 s	5 s	6 s	4 s	4 s	4 s	4 s
	Number of amplicons	49	28	8	8	8	8	6
	% alignment coverage	100	99	93	96	97	96	92
	Mean mismatches per primer	0.027	0.73	1.63	1.48	1.63	2.60	3.04

Running times were analyzed on the same hardware (i7 1185G7 4×3 GHz, 32 GB DDR4 RAM, Ubuntu 22.04.3). Moreover, the number of amplicons, alignment coverage and mean mismatches with alignment sequences are summarized.