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Table 7 Percent of one million reads of lengths 36, 51, 76, 100, and 150 and of divergence 0.1 with gaps mapped correctly to the E.coli genome

From: MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Read

BWA

NGM

NGM+

NGM+

NGM+

length

  

MaxSSmap_fast

MaxSSmap

CUDA-SW++

36

1.2 (0)

33.3 (10.5)

34 (16.5)

43.8 (18.1)

53.2 (17.1)

51

11.4 (0.2)

50.5 (3)

53.3 (8.8)

71.2 (7.5)

79.5 (6.2)

76

38.4 (.7)

70.2 (1.5)

76.5 (4.3)

92.9 (2.7)

96.6 (1.8)

100

62.4 (1)

82.6 (1.4)

91 (2.2)

96.8 (1.9)

98.1 (1.5)

150

76 (1.1)

82.5 (1.2)

92 (2.2)

93.8 (2.2)

94.7 (2.1)

Time in minutes to map reads

36

0.09

0.3

26.6

37.8

315.9

51

0.11

0.5

26.6

38.2

284.9

76

0.15

0.6

19.8

28.4

201.9

100

0.22

0.7

14.8

21

129.9

150

0.34

0.9

19.6

29.2

173.8

  1. Shown in parenthesis are incorrectly mapped reads and remaining are rejected. We denote NextGenMap by NGM.