Skip to main content

Table 3 Assembly results for Bordetella

From: Parallelized short read assembly of large genomes using de Bruijn graphs

  PASHA Velvet ABySS SOAPdenovo
no. of scaffolds 228 294 287 298
NG50 24,517 18,063 18,150 17,870
NG80 10,006 8,237 9,215 8,157
max 121,801 75,085 75,809 74,881
mean 16,508 12,797 13,520 12,583
genome coverage 70.44% 68.45% 53.67% 72.45%
incorrect contigs (mean) 166(5,521) 150(6,834) 138(12,172) 81(10,261)
time (in seconds) 207 292 484 293
  1. PASHA uses the parameters "k = 31", Velvet uses "k = 31, -exp_cov = auto, -cov_cutoff = auto", ABySS uses "k = 31, n = 10" and SOAPdenvo uses "k = 25, insert_length = 198".