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Table 3 Results summary of simulated data

From: A comprehensive evaluation of assembly scaffolding tools

Scaffolder

Read mapper

10 kb contigsa

3 kb contigs

  

Short fragment reads

Long fragment reads

Short fragment reads

Long fragment reads

  

% Correct joins found

Score

% Correct joins found

Score

% Correct joins found

% Joins incorrect

Score

% Correct joins found

% Joins incorrect

Score

ABySS

abyss-map

100.0

1.00

66.7

0.91

98.9

0.0

1.00

99.5

0.0

1.00

Bambus2

Bowtie 2

100.0

1.00

66.7

0.91

63.7

0.0

0.84

95.9

0.0

0.99

BWA

48.2

0.82

48.2

0.87

59.6

0.0

0.82

96.2

0.0

0.99

MIP

Bowtie -v 0

100.0

1.00

96.3

0.99

98.9

0.0

1.00

98.4

0.0

1.00

Bowtie -v 3

100.0

1.00

96.3

0.99

98.4

0.0

0.99

97.9

0.0

1.00

Bowtie 2

100.0

1.00

29.6

0.82

96.3

0.5

0.74

98.7

0.5

0.96

BWA

100.0

1.00

33.3

0.83

98.0

1.1

0.54

98.2

0.4

0.96

Opera

Bowtie

100.0

1.00

92.6

0.98

98.4

0.0

0.99

1.0

10.0

0.79

BWA

100.0

1.00

92.6

0.98

99.8

0.2

0.93

1.2

80.0

0.37

SCARPA

Bowtie -v 0

100.0

1.00

96.3

0.99

98.9

0.0

1.00

95.0

0.0

0.99

Bowtie -v 3

100.0

1.00

96.3

0.99

98.6

0.0

0.99

96.3

0.0

0.99

Bowtie 2

85.2

0.95

96.3

0.99

96.8

0.0

0.99

76.3

0.7

0.92

BWA

85.2

0.95

92.6

0.98

96.6

0.0

0.98

77.9

0.4

0.93

SGA

Bowtie 2

100.0

1.00

96.3

0.99

97.3

0.0

0.99

97.6

0.0

1.00

BWA

100.0

1.00

92.6

0.98

99.0

0.0

1.00

96.2

0.0

0.99

SOAP2

SOAP2

96.3

0.99

96.3

0.99

98.6

0.0

0.99

99.5

0.0

1.00

SOPRA

Bowtie -v 0

100.0

1.00

96.3

0.99

98.3

0.0

0.99

98.2

0.0

1.00

Bowtie -v 3

100.0

1.00

96.3

0.99

97.2

0.0

0.99

97.2

0.0

1.00

Bowtie 2

74.1

0.91

100.0

1.00

91.5

0.5

0.82

85.6

0.5

0.93

BWA

74.1

0.91

88.9

0.97

92.9

0.2

0.89

83.1

0.4

0.93

SSPACE

Bowtie -v 0

100.0

1.00

92.6

0.98

99.1

0.0

1.00

99.6

0.0

1.00

 

Bowtie -v 3

100.0

1.00

92.6

0.98

98.7

0.0

0.99

99.3

0.0

1.00

  1. aNo incorrect joins were made by any of the tools.