Table 4

E. coli correctness on GAGE metrics
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

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 <a onClick="popup('http://genomebiology.com/2013/14/9/R101/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://genomebiology.com/2013/14/9/R101/mathml/M2">View MathML</a> . Indels >5 bp: the number of indels >5 bp reported by GAGE metrics [37]. Assemblies were generated as in Tables 2 and 3.

Koren et al.

Koren et al. Genome Biology 2013 14:R101   doi:10.1186/gb-2013-14-9-r101

Open Data