Skip to main content

Table 3 Scalability of our algorithm for up to 128 million reads. Since our test dataset contained only 8 million reads, we generated these reads randomly, each read was of size 35 and k = 33 was used.

From: Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

reads p user time
(ticks)
sys time
(ticks)
wall time
(min:sec)
16777216 2 37147 259 1:14.02
33554432 2 148070 1219 2:42.66
67108864 2 340653 2348 6:18.77
134217728 2 770922 5560 15:00.42
16777216 4 37254 85 0:38.95
33554432 4 99067 677 1:48.60
67108864 4 240861 1931 4:14.57
134217728 4 471196 4272 8:29.62
16777216 8 20217 57 0:21.90
33554432 8 47319 322 0:55.41
67108864 8 153782 1781 2:39.18
134217728 8 314281 3456 5:17.65
16777216 16 16951 55 0:19.73
33554432 16 17936 135 0:25.64
67108864 16 64408 804 1:10.91
134217728 16 135562 2148 2:21.83
16777216 32 12901 40 0:16.38
33554432 32 9973 191 0:17.55
67108864 32 46659 486 0:53.32
134217728 32 82414 950 1:28.87