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Table 2 Evaluation of dnaasm in comparison to ABySS, Velvet and SPAdes assembler

From: De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application

Sample Assembler Type No. of N50 [bp] Max [bp] Avg. Avg.
   of output contigs    mis. indels
ERR351243 ABySS unitigs 79 40021 224368 0.00 1.61
  Velvet unitigs 206 12813 38818 0.31 0.81
  SPAdes unitigs 43 61281 287932 0.93 2.28
  dnaasm unitigs 84 30628 191880 0.06 1.98
  ABySS scaffolds 33 65136 224368 1.59 2.69
  Velvet scaffolds 30 82451 224509 1.42 3.15
  SPAdes scaffolds 27 74784 333212 1.23 2.53
  dnaasm scaffolds 34 61265 333846 0.62 3.82
SRR1981622 ABySS unitigs 81 36448 110990 1.11 0.99
  Velvet unitigs 254 8636 27708 1.12 0.37
  SPAdes unitigs 53 58976 228504 1.42 1.29
  dnaasm unitigs 73 45793 134195 0.93 1.11
  ABySS scaffolds 40 67391 207675 4.89 1.96
  Velvet scaffolds 33 114376 285632 4.99 2.65
  SPAdes scaffolds 35 98439 228504 3.26 2.09
  dnaasm scaffolds 39 91627 228504 3.33 1.73
SRR1981619 ABySS unitigs 80 36449 110993 8.36 2.85
  Velvet unitigs 314 7163 22826 7.92 1.56
  SPAdes unitigs 53 58765 228586 9.00 3.21
  dnaasm unitigs 77 43959 134261 7.76 2.77
  ABySS scaffolds 43 79578 111309 16.00 4.15
  Velvet scaffolds 35 107026 492812 10.06 4.32
  SPAdes scaffolds 34 98351 228586 8.99 4.31
  dnaasm scaffolds 38 93136 256270 11.21 4.25
SRR5431732 ABySS unitigs 559 11471 57586 17.85 2.90
  Velvet unitigs 1032 4790 18304 17.98 2.57
  SPAdes unitigs 238 30607 129385 21.02 3.74
  dnaasm unitigs 416 16178 59383 21.68 4.10
  ABySS scaffolds 208 35552 131767 19.81 4.51
  Velvet scaffolds 202 41843 182297 21.99 7.21
  SPAdes scaffolds 172 46834 159097 22.65 4.72
  dnaasm scaffolds 354 19644 120052 25.13 4.42
  1. Unitigs output depicts assembling mode without using paired-end tags, scaffolds - with paired reads. The table shows that the presented de novo assembler works comparatively in terms of the number of contigs, N50 statistic, the largest contig length and the quality (average number of mismatches and indels per 100000 aligned bases) of the resultant DNA sequences