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Table 4 E. coli correctness on GAGE metrics

From: Reducing assembly complexity of microbial genomes with single-molecule sequencing

Organism Assembled by Number of contigs N50 Number of structural differences Number of discordant bases QV Number of indels > 5 bp
E. coli K12 MiSeq 100× 139 113,852 1 59 49.00 4
  454 50× 93 117,490 2 26 52.45 0
  MiSeq 100× + 200× CLR 2 2,367,319 2 11 56.26 2
  454 50× + 200× CLR 1 4,649,004 2 11 56.26 2
  CCS 25X + 200× CLR 1 4,653,267 0 14 55.22 2
  200× CLR 1 4,653,486 0 14 55.22 2
  1. Organism: the genome being assembled. Assembled by: the short-read data used for correction and/or assembly. Number of contigs: the number of contigs comprising the assembly. N50: N such that 50% of the genome is contained in contigs of length ≥N. Number of structural differences: the sum of inversions, relocations, and translocations versus the reference using GAGE metrics [37]. Number of discordant bases: total number of different bases when compared to the reference. QV: estimated from the number of indels and SNPs as log 10 assembly length # incorrect bases * 10 . Indels >5 bp: the number of indels >5 bp reported by GAGE metrics [37]. Assemblies were generated as in Tables 2 and 3.