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Table 2 GAGE statistics (contiguity, duplication and compression) on Staphylococcus aureus.

From: GAM-NGS: genomic assemblies merger for next generation sequencing

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
  1. 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.
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