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Table 3 Comparison of various error correction software

From: Pollux: platform independent error correction of single and mixed genomes

 

Illumina MiSeq - E. coli

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

93.81

1.28

0.89

3.01

Quake

58.78

0.05

0.92

4.09

SGA

78.65

0.09

1.11

15.51

BLESS

83.21

0.10

0.00

0.86

Musket

81.75

0.15

0.00

2.37

RACER

86.59

1.60

0.00

1.07

 

Illumina genome analyzer II - S. aureus

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

87.04

0.38

31.73

3.67

Quake

75.30

0.10

29.81

4.81

SGA

47.45

0.02

10.71

14.28

BLESS

55.32

0.06

0.00

0.49

Musket

45.04

0.14

0.00

6.96

RACER

75.76

0.28

0.00

0.68

 

Illumina HiSeq - L. pneumophila

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

96.16

0.13

6.01

14.40

Quake

99.66

0.00

4.25

22.25

SGA

84.61

0.03

3.87

73.82

BLESS

87.61

0.03

0.00

3.56

Musket

83.33

0.10

0.00

18.67

RACER

94.09

0.16

0.00

4.14

 

Illumina HiSeq - M. tuberculosis

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

69.98

0.83

6.51

4.24

Quake

68.06

0.12

3.06

5.62

SGA

31.99

0.16

0.46

17.75

BLESS

60.01

0.13

0.00

1.04

Musket

44.68

0.80

0.00

5.93

RACER

65.14

1.28

0.00

0.79

 

Roche 454 GS Junior - E. coli

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

81.02

4.14

0.82

5.45

Quake

0.21

0.00

0.07

3.62

SGA

8.94

3.63

1.64

5.33

BLESS

34.68

1.27

0.00

0.24

Musket

0.00

0.00

0.00

0.05

RACER

82.03

24.27

0.00

0.36

 

Ion torrent PGM - E. coli

 

Errors

Errors

Reads

Run

Software

corrected (%)

introduced (%)

removed (%)

time (min)

Pollux

87.83

3.43

10.90

26.75

Quake

12.35

2.03

37.60

11.11

SGA

5.43

1.12

0.16

55.93

BLESS

22.82

0.52

0.00

1.25

Musket

9.40

4.88

0.00

47.27

RACER

67.86

15.95

0.00

1.64

  1. The evaluation is performed by aligning corresponding uncorrected reads and corrected reads, which were not removed, against a reference genome using SMALT. Corrected errors are an aggregate of all alignment errors which are found in uncorrected reads but not in corrected reads. Similarly, introduced errors are an aggregate of all alignment errors found in corrected reads but not in uncorrected reads and are relative to the sum of corrected and uncorrected errors. The percentage of reads removed by each software is noted. We note that Quake, SGA, and Musket were intended to only correct Illumina sequencing data.