|
Runtime parameters and speedup for MUMmerGPU test workloads. MUMmerGPU is consistently more than 3 times faster than mummer for a variety of sequencing data. |
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| Reference |
Reference length (bp) |
# of queries |
Query length mean ± stdev. |
Min alignment length (l) |
# of suffix trees (k) |
Speedup |
|
|
||||||
| C. briggsae Chr. III (Sanger) |
13,163,117 |
2,357,666 |
717.84 ± 159.44 |
100 |
2 |
3.71 |
| L. monocytogenes (454) |
2,944,528 |
6,620,471 |
200.54 ± 60.51 |
20 |
1 |
3.79 |
| S. suis (Illumina/Solexa) |
2,007,491 |
26,592,500 |
35.96 ± 0.27 |
20 |
1 |
3.47 |
Schatz et al. BMC Bioinformatics 2007 8:474 doi:10.1186/1471-2105-8-474 |
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