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Table 3 Evaluation of assemblies of the simulated dataset (100×, 36 bp, 1% error) and dataset D1 with CloudBrush, Contrail, Velvet, and Edena

From: A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework

Dataset Assembler # of contigs1 N50 Largest contig size Precision Recall # of valid
contigs1
# of invalid contigs1 Runtime
(sec)
100 × 36 bp
1% error
CloudBrush 447 17907 95387 99.79% 97.51% 420 27 6218
  Contrail 906 8982 40066 99.72% 96.76% 858 48 5499
  Velvet 507 15632 100501 99.68% 96.95% 498 9 590
  Edena 4012 1436 11264 98.84% 91.85% 3868 144 2524
D1 dataset CloudBrush 521 15149 66832 99.26% 97.10% 481 40 5555
  Contrail 930 8605 40066 99.73% 96.81% 886 44 4789
  Velvet 505 15862 73042 99.62% 96.90% 494 11 452
  Edena 889 9045 44942 99.18% 96.34% 823 66 1401
  1. 1 Contigs with lengths > 200 bp are counted.