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Table 1 Evaluation of Assemblathon1 dataset assemblies

From: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

  Contig N50 Contig path NG50 Scaffold N50 Scaffold path NG50 Number of Structural Error Substitution Error rate Copy Number Error rate Genome coverage (%) Memory (G) Run time (h)
V1 207,783 13,357 329,384 13,539 14,306 5.40E-05 9.14E-03 98.8 46 7
V1.05* 343,889 82,264 1,684,436 116,651 1,878 1.20E-05 6.75E-03 98.8 20 8
V2.0 357,238 111,365 15,077,357 170,432 1,414 4.25E-06 2.79E-03 98.8 20 10§
ALLPATHS-LG* 163,633 72,480 8,185,650 210,649 1,244 2.92E-06 6.71E-02 98.3 100 12
  1. Contig and scaffold path NG50 were defined in Assemblathon1[1].
  2. *SOAPdenovo v1.05 and ALLPATHS-LG’s evaluation result data were from[1].
  3. §Time spent on filtering contamination was not included.