Table 8

GAGE statistics (contiguity, duplication and compression) on human chromosome 14.

Assembler

Ctg num

NG50 (kb)

NG50 corr. (kb)

Assembly size (%)

Chaff size (%)

Unaligned ref (%)

Unaligned asm (%)

Dupl (%)

Comp (%)


Allpaths-LG

4529

27.96

15.69

78.67

0.02

20.03

0.04

0.23

2.11

CABOG

3361

35.86

18.63

80.34

0.02

19.13

0.07

0.13

1.39


Allpaths-LG + CABOG

GAM-NGS

2235

61.64

21.91

80.94

0.02

19.08

0.10

0.88

1.43

GAA

1989

69.40

23.04

82.08

0.02

18.92

0.09

1.52

1.39


CABOG + Allpaths-LG

GAM-NGS

1979

66.29

23.63

81.00

0.02

19.00

0.06

0.74

1.37

GAA

1903

70.39

23.89

81.89

0.02

18.98

0.07

1.21

1.36


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 statistics were computed using the same script with the gapped reference genome (107,349,540 bp).

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

Open Data