Table 3.

Accuracy of pairwise alignment algorithms

		HiSeq		ONT		l = 1K, d = 5%		l = 10K, d = 5%
		Time	Recall	Time	Recall	Time	Recall	Time	Recall
BWA-MEM	WFA	0.06	100	2.46	100	0.93	100	7.28	100
	WFA-Adap	0.07	100	1.51	99.8	0.68	100	0.68	100
	Gaba	1.26	100	error	error	0.74	95.2	0.81	94.8
	KSW2-Z2	2.42	100	15.23	100	16.47	100	188.4	100
	KSW2-D2	2.87	100	18.13	100	19.64	100	219.6	100
Bowtie2	WFA	0.07	100	4.80	100	1.60	100	12.05	100
	WFA-Adap	0.08	100	3.18	99.8	1.32	100	1.25	100
	Gaba	1.26	100	error	error	0.74	95.4	0.66	95.4
	KSW2-Z2	2.40	100	15.21	100	16.46	100	190.8	100
	KSW2-D2	2.91	100	18.16	100	19.66	100	220.8	100

Note: Time (in seconds) and recall (as percentage of the total sequences aligned) for error-sensitive algorithms. Two different penalty schemes were used: first corresponding to the default values used by BWA-MEM (i.e. $x=4,o=6,e=2$), and second matching Bowtie2’s end-to-end alignment scores (i.e. $x=6,o=5,e=3$).