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Table 5 Runtime and main memory usage for finding nodes

From: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

k   62 E. coli 7 × Chr1 7 × HG
50 A4 3 (1.81) 9 (1.28) 9 (1.96)
50 A4compr1 3 (1.52) 9 (0.98) 11 (1.66)
50 A4compr2 6 (1.20) 20 (0.70) 29 (1.39)
100 A4 3 (1.78) 12 (1.26) 27 (1.94)
100 A4compr1 3 (1.49) 15 (0.97) 19 (1.64)
100 A4compr2 6 (1.17) 31 (0.68) 51 (1.37)
500 A4 9 (1.73) 20 (1.26) 22 (1.93)
500 A4compr1 12 (1.43) 24 (0.96) 27 (1.63)
500 A4compr2 17 (1.11) 55 (0.67) 74 (1.36)
  1. The first column shows the k-mer size and the second column specifies the algorithm used in the experiment. The remaining columns show the run-times in seconds for finding the nodes corresponding to 10,000 patterns of length 900 (that occur in the pan-genome) and, in parentheses, the maximum main memory usage in bytes per base pair for the data sets described in the text