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Table 3 Sensitivity, specificity and F1 score for the classification of k-mers into trusted and untrusted subsets

From: Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

 

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

  1. 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