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Table 2 Evaluating the short-read only assemblies

From: Efficient and accurate whole genome assembly and methylome profiling of E. coli

Assembler Data type kmer Approx. coverage Avg identity Indels<5 bp Indels>= 5 bp Inversions Unalignable contigs Relocations SNPs
Velvet MiSeq 59 100X 99.99 13 38 2 0 16 42
   59 75X 99.99 23 31 0 0 12 110
   59 50X 99.99 18 36 1 0 17 88
   59 25X 99.99 36 129 0 0 8 96
Ray MiSeq 36 100X 100 1 6 2 19 2 9
   36 75X 99.99 5 10 0 11 2 35
   36 50X 99.99 2 3 0 8 2 26
   36 25X 100 5 5 1 4 4 41
  Ion 29 100X 99.86 5645 29 0 4 1 67
   29 75X 99.9 4209 14 0 4 1 58
   29 50X 99.93 2784 7 0 0 0 58
   29 25X 99.95 1933 3 0 1 1 54
MIRA MiSeq n/a 100X 99.99 8 6 13 2 15 73
   n/a 75X 99.99 20 4 11 0 11 124
   n/a 50X 99.99 31 5 15 0 9 113
   n/a 25X 99.99 9 7 7 0 7 81
  Ion n/a 100X 99.98 207 6 11 4 11 50
   n/a 75X 99.98 239 8 14 2 9 42
   n/a 50X 99.98 292 10 9 1 8 58
   n/a 25X 99.98 524 10 9 0 3 34
  1. The bolded assemblies represent the best assembly for the specified combination of sequencer and software.