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Table 5 GAGE statistics (contiguity, duplication and compression) on Rhodobacter sphaeroides.

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 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
  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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