Table 2

Performance comparison of Bustard, Ibis and AYB on several sets of reads of varying read length and chemistry versions.

Reads mapped, %

Reads perfect, %

Bustard

Ibis

Δ%

AYB

Δ%

Bustard

Ibis

Δ%

AYB

Δ%


ϕX174 L2

76.62

78.33

+2.23

78.25

+2.13

55.88

58.94

+5.48

62.29

+11.48

ϕX174 L4

63.02

66.11

+4.90

65.09

+3.29

40.09

43.08

+7.46

44.74

+11.60

ϕX174 L6

72.09

74.07

+2.75

74.08

+2.77

51.19

53.34

+4.20

56.00

+9.40

Ibis Test

84.77

88.45

+4.34

88.19

+4.03

44.34

66.14

+49.16

69.32

+56.34

B. pert./1

28.76

39.16

+35.94

45.80

+58.98

2.53

3.14

+23.70

4.13

+62.86

... trimmed

77.35

81.06

+4.80

81.14

+4.90

39.52

47.64

+20.55

55.24

+39.79

B. pert./2

34.33

47.41

+38.75

53.50

+55.57

6.22

17.69

+183.98

26.67

+327.97

... trimmed

66.54

70.22

+5.53

72.07

+8.31

30.13

40.72

+35.18

48.25

+60.15

BGI/1

87.41

89.01

+1.82

88.85

+1.64

59.62

68.39

+14.70

69.29

+16.22

BGI/2

84.58

86.29

+2.03

86.52

+2.29

55.95

61.90

+10.64

63.30

+13.14

Illumina/1

97.58

97.80

+0.22

97.85

+0.28

72.55

75.80

+4.49

76.70

+5.73

Illumina/2

96.29

96.73

+0.46

96.82

+0.55

70.61

73.88

+4.63

74.66

+5.74

HiSeq/1

84.97

85.24

+0.32

85.97

+1.18

60.29

62.55

+3.75

64.50

+6.98

HiSeq/2

79.78

81.34

+1.76

49.79

55.58

+11.63


Performance is compared in terms of the percentage of reads mapped back to the reference with five edits or fewer, and the percentage of reads which perfectly match the reference; the 'Δ%' figures for Ibis and AYB, where given, are the percentage improvements over Bustard. See text for further details. †Ibis failed to process the second end of the HiSeq data.

Massingham and Goldman Genome Biology 2012 13:R13   doi:10.1186/gb-2012-13-2-r13

Open Data