Table 1 Runtime parameters and speedup for MUMmerGPU test workloads. MUMmerGPU is consistently more than 3 times faster than mummer for a variety of sequencing data.
From: High-throughput sequence alignment using Graphics Processing Units
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 |