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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.
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