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Table 1 Rabema benchmark results (normalized found interval) for 100 k simulated reads

From: BitMapper: an efficient all-mapper based on bit-vector computing

Mapper

Time

Benchmark category

        
 

[min:sec]

All[%]

All-best[%]

Any-best[%]

Bowtie2 a

0:18

90.18

97.68

96.60

92.25

95.87

96.46

96.14

94.48

99.26

100.00

99.49

97.51

   

78.95

52.71

21.13

 

93.69

92.76

92.27

 

96.63

96.27

95.38

BWA b

0:49

92.28

100.00

99.81

96.75

98.84

100.00

99.80

99.40

98.89

100.00

99.86

99.50

   

79.47

44.91

16.65

 

93.61

78.42

70.67

 

93.70

78.61

71.17

GEM c

0:14

92.75

98.25

97.65

95.69

98.15

98.27

98.21

97.97

99.36

99.42

99.42

99.24

   

88.44

67.06

33.44

 

98.11

96.87

95.87

 

99.42

98.74

97.33

Bowtie 2

—

99.73

100.00

100.00

100.00

99.97

100.00

100.00

100.00

99.97

100.00

100.00

100.00

   

99.96

99.53

95.45

 

99.95

99.67

97.89

 

99.95

99.67

97.89

BWA

40:32

97.80

100.00

99.97

99.62

98.95

100.00

99.97

99.62

98.95

100.00

99.97

99.62

   

94.26

83.53

75.30

 

93.82

79.03

70.93

 

93.82

79.16

71.17

GEM

3:15

96.02

98.25

98.24

98.09

98.15

98.27

98.18

98.01

99.35

99.42

99.41

99.24

   

95.92

87.02

66.35

 

98.17

97.02

95.94

 

99.44

98.68

97.17

Masai

17:43

99.86

100.00

100.00

100.00

99.96

100.00

100.00

100.00

99.97

100.00

100.00

100.00

   

99.87

99.54

97.87

 

99.85

99.29

98.59

 

99.85

98.34

98.70

Hobbes 2

7:51

99.82

99.98

99.97

99.97

99.97

99.98

99.97

99.97

99.99

100.00

99.99

99.98

   

99.98

99.87

97.20

 

99.97

99.98

99.80

 

99.97

100.00

99.92

mrFAST

12:32

99.32

100.00

100.00

100.00

99.42

100.00

100.00

100.00

99.43

100.00

100.00

100.00

   

100.00

99.96

87.51

 

100.00

100.00

53.69

 

100.00

100.00

54.09

RazerS 3 d

41:33

99.92

100.00

100.00

100.00

99.99

100.00

100.00

100.00

99.99

100.00

100.00

100.00

   

100.00

99.84

98.62

 

100.00

99.95

99.92

 

100.00

99.95

99.92

RazerS 3

54:59

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

   

100.00

100.00

100.00

 

100.00

100.00

100.00

 

100.00

100.00

100.00

Yara

3:06

—

—

—

—

—

—

—

—

—

—

—

—

   

—

—

—

 

—

—

—

 

—

—

—

BitMapper

2:57

99.99

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

100.00

   

100.00

99.99

99.98

 

100.00

100.00

100.00

 

100.00

100.00

100.00

  1. Bowtie2 a, BWA b, and GEM c represent the results in default sensitivity mode, while Bowtie2, BWA, and GEM represent the results in high sensitivity mode. The RazerS 3 d and RazerS 3 represent the results of RazerS 3 in default and full sensitivity mode, respectively. Note that in default mode, RazerS 3 is designed to find 99% of mapping locations, while Bowtie2, BWA, and GEM are designed to find the best mapping locations for each reads