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Table 1 Speed and percentage speed up of each Bowtie2 variant on GCAT benchmarks

From: Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

Single ended

     

Length

Number

Bowtie2 2.0.0

Correct

Mapped

Bowtie2 GP

Correct

Mapped

speedup %

100

11945249

684 ± 6

89.23%

98.88%

782 ± 7

89.05%

98.25%

14

150

7963499

556 ± 2

93.58%

99.48%

696 ± 5

93.20%

98.58%

25

250

4778100

413 ± 9

97.14%

99.74%

509 ± 11

96.04%

98.33%

23

400

2986312

342 ± 19

98.77%

99.86%

371 ± 29

96.50%

97.69%

8

Length

Number

Bowtie2 2.0.0

Correct

Mapped

Bowtie2 GP

Correct

Mapped

speedup %

100

11945249

486 ± 6

93.54%

98.81%

640 ± 16

92.98%

98.16%

32

150

7963499

481 ± 3

96.33%

99.48%

701 ± 3

95.46%

98.55%

46

250

4778100

462 ± 12

98.54%

99.82%

656 ± 23

97.05%

98.40%

42

400

2986312

425 ± 41

99.36%

99.94%

524 ± 65

96.87%

97.76%

23

Paired end

     

Length

Number

Bowtie2 2.0.0

Correct

Mapped

Bowtie2 GP

Correct

Mapped

speedup %

100

5972625

674

94.47%

99.41%

827

94.03%

98.70%

23

150

3981750

736

91.99%

98.82%

956

91.61%

97.62%

30

250

2389050

826

95.46%

98.96%

1041

94.38%

97.33%

26

400

1493156

658

97.79%

99.24%

822

95.65%

97.08%

25

Length

Number

Bowtie2 2.2.3

Correct

Mapped

Bowtie2 GP 2.2.3

Correct

Mapped

speedup %

100

5972625

702

95.19%

98.91%

921

94.74%

98.20%

31

150

3981750

717

93.53%

98.93%

999

93.07%

97.66%

39

250

2389050

763

95.49%

98.61%

1044

94.21%

96.83%

37

400

1493156

461

98.29%

99.39%

616

95.97%

97.24%

34

  1. To normalise for different sequence lengths, we report millions of DNA bases processed per CPU hour. (In paired end tests both ends are counted.) Where available ± gives estimated standard deviation. The percentage of correctly assigned sequences and the percentage mapped are both reported by GCAT.