Table 3.

Sensitivity, specificity and F₁ score for the classification of k-mers into trusted and untrusted subsets

	10× cov				25× cov				50× cov
	sens	spec	F1		sens	spec	F1		sens	spec	F1
	S. enterica
Quake	0	100	0		93.77	100	96.78		99.31	99.97	99.65
BayesHammer	98.22	99.42	98.81		99.22	99.98	99.60		99.42	99.98	99.71
Detox	98.46	99.21	98.82		99.51	99.95	99.74		99.75	99.96	99.87
	P. aeruginosa
Quake	4.64	100	8.88		80.58	100	89.24		98.08	100	99.03
BayesHammer	99.07	99.64	99.11		99.25	99.99	99.62		99.23	100	99.61
Detox	99.23	99.69	99.25		99.80	99.97	99.88		99.90	99.97	99.94
	C. elegans
Quake	n/a	n/a	n/a		n/a	n/a	n/a		91.68	99.94	95.65
BayesHammer	96.64	98.71	97.40		96.49	99.88	98.18		96.34	99.95	98.13
Detox	99.20	98.96	98.87		99.81	99.69	99.82		99.91	99.68	99.91
	A. thaliana
Quake	0	100	0		94.20	99.99	97.01		99.00	99.96	99.49
BayesHammer	96.34	98.52	96.93		95.88	99.84	97.84		95.11	99.96	97.49
Detox	98.36	97.68	97.68		99.42	99.40	99.49		99.70	99.54	99.76
	H. sapiens chr. 21
Quake	n/a	n/a	n/a		25.06	99.46	39.88		48.96	99.86	65.7
BayesHammer	84.62	99.05	90.53		88.9	99.79	94.01		90.8	99.84	95.12
Detox	90.09	98.39	92.88		95.84	98.47	97.04		97.5	98.41	98.2

Quake and BayesHammer were run with default settings. Our CRF method (Detox) was run at neighbourhood size s=3. For C. elegans at 10× and 25× coverage and H. sapiens, chr. 21, Quake was unable to identify a cutoff and hence, no results are shown (n/a). The highest values are shown in boldface