Table 2

GAGE statistics (contiguity, duplication and compression) on Staphylococcus aureus.

Assembler

Ctg num

NG50 (kb)

NG50 corr. (kb)

Assembly size (%)

Chaff size (%)

Unaligned ref (%)

Unaligned asm (%)

Dupl (%)

Comp (%)


Allpaths-LG

60

96.74

66.23

98.88

0.03

0.61

0.01

0.04

1.26

MSR-CA

94

59.15

48.23

98.60

0.01

1.28

0.00

0.71

0.88


Allpaths-LG + MSR-CA

GAM-NGS

44

141.54

75.82

100.49

0.00

0.44

0.01

0.26

0.99

GAA

40

139.48

80.68

99.52

0.03

0.37

0.01

0.32

0.88

ZORRO

81

74.68

62.85

99.70

0.16

0.32

0.04

0.59

0.88


MSR-CA + Allpaths-LG

GAM-NGS

66

90.47

66.44

100.21

0.01

1.01

0.00

2.03

0.89

GAA

53

131.65

64.43

100.66

0.01

0.95

0.00

1.90

0.79

ZORRO

80

74.64

62.85

99.63

0.14

0.32

0.05

0.53

1.11



Allpaths-LG

60

96.74

66.23

98.88

0.03

0.61

0.01

0.04

1.26

SOAPdenovo

107

288.18

62.68

100.55

0.34

0.22

0.02

1.66

1.45


Allpaths-LG + SOAPdenovo

GAM-NGS

56

107.12

69.39

99.52

0.03

0.56

0.01

0.34

1.26

GAA

40

255.66

83.67

108.10

0.06

0.25

0.01

2.78

1.31

ZORRO

104

76.94

65.83

105.59

0.31

0.15

0.10

5.19

1.36


SOAPdenovo + Allpaths-LG

GAM-NGS

93

288.18

62.68

100.92

0.32

0.20

0.02

1.88

1.40

GAA

74

294.96

62.87

101.92

0.34

0.16

0.02

2.62

1.37

ZORRO

107

76.94

62.68

105.63

0.29

0.16

0.09

5.17

1.50


For each assembler we report the number of contigs greater than 200 bp (Ctg), the NG50, the corrected NG50 (NG50 computed breaking the assembly at each error), assembly's total length, the percentage of short (Chaff) contigs, the length of reference's regions which cannot be found in the assembly (Unaligned ref), the length of assembly's regions that cannot be found in the reference (Unaligned asm), the percentage of duplicated (Dupl) and compressed (Comp) regions in the assembly. All the percentages in the table are computed with respect to the true genome size.

Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6   doi:10.1186/1471-2105-14-S7-S6

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