Table 3

Velvet E. coli assembly

Contigs

N50

N90

Scaffolds

N50

N90

Breaks

Miscalls

Cov


Uncorrected

398

94,827

17,503

380

95,365

23,869

5

456

0.9990

Corrected

345

94,831

25,757

332

95,369

26,561

4

315

0.9992


Velvet assemblies of E. coli 36 bp paired end reads at 152× coverage. After correcting the reads, more reads are included in the assembly into fewer contigs and scaffolds. N50 and N90 values were computed using the genome size 4,639,675 bp. The N50 value was similar for both assemblies, but N90 grew significantly with corrected reads. Correcting the reads also improved the correctness of the assembly producing fewer mis-assembled scaffolds (Breaks) and miscalled bases (Miscalls) and covering a greater percentage of the reference genome (Cov).

Kelley et al. Genome Biology 2010 11:R116   doi:10.1186/gb-2010-11-11-r116

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