| Dataset . | Tool . | Execution time (minutes) . | Speedup . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Number of cores . | Number of cores . | |||||||||
| . | . | 1 . | 4 . | 8 . | 16 . | 32 . | 64 . | 4 . | 8 . | 16 . | 32 . | 64 . |
| D1 | BWA-Threads | 106.6 | 27.6 ± 0.1 | 14.3 ± 0.1 | 10.9 ± 0.0 | — | — | 3.9 | 7.4 | 9.8 | — | — |
| BigBWA (hybrid) | 29.6 ± 0.2 | 15.1 ± 0.3 | 11.8 ± 0.1 | 6.8 ± 0.3 | 3.6 ± 0.1 | 3.6 | 7.0 | 9.0 | 15.7 | 29.6 | ||
| BigBWA | 29.1 ± 0.3 | 15.7 ± 0.1 | 7.9 ± 0.1 | 4.5 ± 0.1 | 3.0 ± 0.1 | 3.7 | 6.8 | 13.4 | 23.5 | 35.5 | ||
| D2 | BWA-Threads | 258.0 | 66.0 ± 0.1 | 33.7 ± 0.1 | 24.9 ± 0.0 | — | — | 3.9 | 7.6 | 10.4 | — | — |
| BigBWA (hybrid) | 69.6 ± 1.3 | 36.4 ± 0.6 | 24.5 ± 0.5 | 15.3 ± 0.1 | 8.8 ± 0.1 | 3.7 | 7.1 | 10.5 | 16.8 | 29.3 | ||
| BigBWA | 69.1 ± 1.4 | 37.5 ± 0.4 | 20.7 ± 0.5 | 10.9 ± 0.3 | 7.2 ± 0.3 | 3.7 | 6.9 | 12.5 | 23.6 | 35.8 | ||
| D3 | BWA-Threads | 3208.6 | 816.8 ± 2.5 | 408.1 ± 1.7 | 333.3 ± 0.3 | — | — | 3.9 | 7.9 | 9.6 | — | — |
| BigBWA (hybrid) | 828.8 ± 9.5 | 431.1 ± 9.0 | 221.9 ± 4.0 | 183.3 ± 2.2 | 107.2 ± 0.8 | 3.9 | 7.4 | 14.5 | 17.5 | 29.9 | ||
| BigBWA | 848.8 ± 13.6 | 444.9 ± 8.2 | 229.2 ± 5.1 | 120.1 ± 1.4 | 87.8 ± 0.2 | 3.8 | 7.2 | 14.0 | 26.7 | 36.6 | ||
| Dataset . | Tool . | Execution time (minutes) . | Speedup . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Number of cores . | Number of cores . | |||||||||
| . | . | 1 . | 4 . | 8 . | 16 . | 32 . | 64 . | 4 . | 8 . | 16 . | 32 . | 64 . |
| D1 | BWA-Threads | 106.6 | 27.6 ± 0.1 | 14.3 ± 0.1 | 10.9 ± 0.0 | — | — | 3.9 | 7.4 | 9.8 | — | — |
| BigBWA (hybrid) | 29.6 ± 0.2 | 15.1 ± 0.3 | 11.8 ± 0.1 | 6.8 ± 0.3 | 3.6 ± 0.1 | 3.6 | 7.0 | 9.0 | 15.7 | 29.6 | ||
| BigBWA | 29.1 ± 0.3 | 15.7 ± 0.1 | 7.9 ± 0.1 | 4.5 ± 0.1 | 3.0 ± 0.1 | 3.7 | 6.8 | 13.4 | 23.5 | 35.5 | ||
| D2 | BWA-Threads | 258.0 | 66.0 ± 0.1 | 33.7 ± 0.1 | 24.9 ± 0.0 | — | — | 3.9 | 7.6 | 10.4 | — | — |
| BigBWA (hybrid) | 69.6 ± 1.3 | 36.4 ± 0.6 | 24.5 ± 0.5 | 15.3 ± 0.1 | 8.8 ± 0.1 | 3.7 | 7.1 | 10.5 | 16.8 | 29.3 | ||
| BigBWA | 69.1 ± 1.4 | 37.5 ± 0.4 | 20.7 ± 0.5 | 10.9 ± 0.3 | 7.2 ± 0.3 | 3.7 | 6.9 | 12.5 | 23.6 | 35.8 | ||
| D3 | BWA-Threads | 3208.6 | 816.8 ± 2.5 | 408.1 ± 1.7 | 333.3 ± 0.3 | — | — | 3.9 | 7.9 | 9.6 | — | — |
| BigBWA (hybrid) | 828.8 ± 9.5 | 431.1 ± 9.0 | 221.9 ± 4.0 | 183.3 ± 2.2 | 107.2 ± 0.8 | 3.9 | 7.4 | 14.5 | 17.5 | 29.9 | ||
| BigBWA | 848.8 ± 13.6 | 444.9 ± 8.2 | 229.2 ± 5.1 | 120.1 ± 1.4 | 87.8 ± 0.2 | 3.8 | 7.2 | 14.0 | 26.7 | 36.6 | ||
Highlighted the best tool for a particular number of cores. These results were obtained using BWA version 0.7.12.
| Dataset . | Tool . | Execution time (minutes) . | Speedup . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Number of cores . | Number of cores . | |||||||||
| . | . | 1 . | 4 . | 8 . | 16 . | 32 . | 64 . | 4 . | 8 . | 16 . | 32 . | 64 . |
| D1 | BWA-Threads | 106.6 | 27.6 ± 0.1 | 14.3 ± 0.1 | 10.9 ± 0.0 | — | — | 3.9 | 7.4 | 9.8 | — | — |
| BigBWA (hybrid) | 29.6 ± 0.2 | 15.1 ± 0.3 | 11.8 ± 0.1 | 6.8 ± 0.3 | 3.6 ± 0.1 | 3.6 | 7.0 | 9.0 | 15.7 | 29.6 | ||
| BigBWA | 29.1 ± 0.3 | 15.7 ± 0.1 | 7.9 ± 0.1 | 4.5 ± 0.1 | 3.0 ± 0.1 | 3.7 | 6.8 | 13.4 | 23.5 | 35.5 | ||
| D2 | BWA-Threads | 258.0 | 66.0 ± 0.1 | 33.7 ± 0.1 | 24.9 ± 0.0 | — | — | 3.9 | 7.6 | 10.4 | — | — |
| BigBWA (hybrid) | 69.6 ± 1.3 | 36.4 ± 0.6 | 24.5 ± 0.5 | 15.3 ± 0.1 | 8.8 ± 0.1 | 3.7 | 7.1 | 10.5 | 16.8 | 29.3 | ||
| BigBWA | 69.1 ± 1.4 | 37.5 ± 0.4 | 20.7 ± 0.5 | 10.9 ± 0.3 | 7.2 ± 0.3 | 3.7 | 6.9 | 12.5 | 23.6 | 35.8 | ||
| D3 | BWA-Threads | 3208.6 | 816.8 ± 2.5 | 408.1 ± 1.7 | 333.3 ± 0.3 | — | — | 3.9 | 7.9 | 9.6 | — | — |
| BigBWA (hybrid) | 828.8 ± 9.5 | 431.1 ± 9.0 | 221.9 ± 4.0 | 183.3 ± 2.2 | 107.2 ± 0.8 | 3.9 | 7.4 | 14.5 | 17.5 | 29.9 | ||
| BigBWA | 848.8 ± 13.6 | 444.9 ± 8.2 | 229.2 ± 5.1 | 120.1 ± 1.4 | 87.8 ± 0.2 | 3.8 | 7.2 | 14.0 | 26.7 | 36.6 | ||
| Dataset . | Tool . | Execution time (minutes) . | Speedup . | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Number of cores . | Number of cores . | |||||||||
| . | . | 1 . | 4 . | 8 . | 16 . | 32 . | 64 . | 4 . | 8 . | 16 . | 32 . | 64 . |
| D1 | BWA-Threads | 106.6 | 27.6 ± 0.1 | 14.3 ± 0.1 | 10.9 ± 0.0 | — | — | 3.9 | 7.4 | 9.8 | — | — |
| BigBWA (hybrid) | 29.6 ± 0.2 | 15.1 ± 0.3 | 11.8 ± 0.1 | 6.8 ± 0.3 | 3.6 ± 0.1 | 3.6 | 7.0 | 9.0 | 15.7 | 29.6 | ||
| BigBWA | 29.1 ± 0.3 | 15.7 ± 0.1 | 7.9 ± 0.1 | 4.5 ± 0.1 | 3.0 ± 0.1 | 3.7 | 6.8 | 13.4 | 23.5 | 35.5 | ||
| D2 | BWA-Threads | 258.0 | 66.0 ± 0.1 | 33.7 ± 0.1 | 24.9 ± 0.0 | — | — | 3.9 | 7.6 | 10.4 | — | — |
| BigBWA (hybrid) | 69.6 ± 1.3 | 36.4 ± 0.6 | 24.5 ± 0.5 | 15.3 ± 0.1 | 8.8 ± 0.1 | 3.7 | 7.1 | 10.5 | 16.8 | 29.3 | ||
| BigBWA | 69.1 ± 1.4 | 37.5 ± 0.4 | 20.7 ± 0.5 | 10.9 ± 0.3 | 7.2 ± 0.3 | 3.7 | 6.9 | 12.5 | 23.6 | 35.8 | ||
| D3 | BWA-Threads | 3208.6 | 816.8 ± 2.5 | 408.1 ± 1.7 | 333.3 ± 0.3 | — | — | 3.9 | 7.9 | 9.6 | — | — |
| BigBWA (hybrid) | 828.8 ± 9.5 | 431.1 ± 9.0 | 221.9 ± 4.0 | 183.3 ± 2.2 | 107.2 ± 0.8 | 3.9 | 7.4 | 14.5 | 17.5 | 29.9 | ||
| BigBWA | 848.8 ± 13.6 | 444.9 ± 8.2 | 229.2 ± 5.1 | 120.1 ± 1.4 | 87.8 ± 0.2 | 3.8 | 7.2 | 14.0 | 26.7 | 36.6 | ||
Highlighted the best tool for a particular number of cores. These results were obtained using BWA version 0.7.12.
This PDF is available to Subscribers Only
View Article Abstract & Purchase OptionsFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.
