Table 5

GAGE statistics (contiguity, duplication and compression) on Rhodobacter sphaeroides.

Assembler

Ctg num

NG50 (kb)

NG50 corr. (kb)

Assembly size (%)

Chaff size (%)

Unaligned ref (%)

Unaligned asm (%)

Dupl (%)

Comp (%)


Allpaths-LG

204

42.45

34.42

99.68

0.01

0.45

0.01

0.38

0.31

MSR-CA

395

22.12

19.08

97.02

0.01

3.47

0.04

1.05

0.53


Allpaths-LG + MSR-CA

GAM-NGS

168

51.12

37.88

99.97

0.00

0.28

0.01

0.61

0.31

GAA

164

53.82

40.55

100.07

0.01

0.20

0.01

0.63

0.32

ZORRO

216

38.87

30.64

100.41

0.03

0.36

0.02

0.43

0.48


MSR-CA + Allpaths-LG

GAM-NGS

199

49.61

37.88

97.95

0.01

3.10

0.04

1.58

0.61

GAA

177

54.71

40.55

99.74

0.01

1.61

0.04

1.08

0.35

ZORRO

206

44.61

38.79

101.14

0.09

0.21

0.06

1.64

0.25



Bambus2

177

93.19

12.78

94.97

0.00

4.92

0.01

0.00

0.24

SOAPdenovo

202

131.68

14.34

100.29

0.44

0.76

0.01

1.30

0.46


Bambus2 + SOAPdenovo

GAM-NGS

83

149.75

14.16

98.32

0.00

3.02

0.00

1.59

0.63

GAA

100

194.16

14.74

98.35

0.13

2.28

0.01

0.63

0.58

ZORRO

711

16.56

13.18

100.48

0.89

0.66

0.25

1.05

0.59


SOAPdenovo + Bambus2

GAM-NGS

177

154.47

15.17

100.41

0.42

0.82

0.01

1.67

0.48

GAA

174

188.18

14.54

100.35

0.44

0.76

0.01

1.38

0.48

ZORRO

720

16.56

12.78

100.48

0.84

0.69

0.24

1.14

0.56


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

Open Data