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Table 1 Comparison of runtime between the JA algorithm and our algorithm on an input with 8 million reads from a plant genome

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

   JA ALGO ParBiConstruct
P k U(sec) S(sec) R(mm:ss) U(sec) speedup S(sec) speedup R(mm:ss) Speedup
8 21 6388.08 21.54 13:26.42 1028.61 6.21 8.08 2.67 2:10.77 6.17
8 27 2220.41 14.85 5:47.71 500.22 4.44 3.72 3.99 1:04.12 5.42
8 33 1662.14 6.63 3:29.89 288.14 5.77 2.47 2.68 0:37.46 5.60
8 35 496.89 3.81 1:03.77 159.59 3.11 1.03 3.70 0:21.19 3.01
12 21 9116.72 20.31 12:43.14 985.97 9.25 6.91 2.94 1:23.95 9.09
12 27 2626.30 13.94 3:59.85 479.10 5.48 3.20 4.36 0:41.32 5.80
12 33 2320.07 6.14 3:15.15 317.08 7.32 2.35 2.61 0:27.76 7.03
12 35 561.02 3.47 0:48.19 166.06 3.38 1.13 3.07 0:15.04 3.20
16 21 11943.18 19.91 12:29.49 1044.31 11.44 7.42 2.68 1:06.91 11.20
16 27 2889.32 12.95 3:50.81 498.36 5.80 3.42 3.79 0:32.48 7.11
16 33 2971.37 6.49 3:07.41 357.63 8.31 2.53 2.57 0:23.64 7.93
16 35 580.08 3.67 0:37.63 170.56 3.40 1.33 2.76 0:11.85 3.18
24 21 17744.55 20.26 12:21.94 1205.51 14.72 8.00 2.53 0:51.74 14.34
24 27 3399.06 15.24 2:39.02 658.02 5.17 4.00 3.81 0:28.72 5.54
24 33 4981.96 7.89 6:25.41 652.80 7.63 3.69 2.14 0:51.65 7.46
24 35 750.26 5.57 0:37.30 295.58 2.54 2.23 2.50 0:14.19 2.63
32 21 23119.80 20.95 12:04.89 1070.31 21.60 8.40 2.49 0:34.90 20.77
32 27 3897.63 15.20 2:12.96 464.24 8.40 5.21 2.92 0:15.81 8.41
32 33 5132.44 9.33 3:11.64 534.38 9.60 4.84 1.93 0:21.01 9.12
32 35 973.78 5.35 0:37.30 324.23 3.00 3.35 1.60 0:13.16 2.83
48 21 37116.65 26.37 13:03.67 2422.83 15.32 13.46 1.96 0:55.33 14.16
48 27 4932.47 21.70 1:48.76 1112.72 4.43 10.51 2.06 0:26.11 4.17
48 33 6658.10 13.72 3:11.84 1157.33 5.75 9.41 1.46 0:34.33 5.59
48 35 1020.88 10.95 0:30.47 447.84 2.28 8.18 1.34 0:14.08 2.16
64 21 51443.09 35.46 16:25.33 1938.25 26.54 25.05 1.42 0:39.57 24.90
64 27 6304.66 33.49 2:05.96 1029.89 6.12 21.80 1.54 0:21.64 5.82
64 33 15314.25 23.95 5:57.82 673.55 22.74 21.31 1.12 0:17.08 20.95
64 35 1048.56 20.71 0:25.93 358.62 2.92 18.86 1.10 0:09.87 2.63
  1. Input Reads: 8388608 short reads, each of size 36 base pairs
  2. Average User time speed up = 8.310X
  3. Average System time speed up = 2.490X
  4. Average Real time speed up = 8.079X