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.

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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