Table 5

Execution time comparison among different thread conditions
36 bp read data set 76 bp read data set 100 bp read data set
Threads 1 2 4 1 2 4 1 2 4
Hybrid aligner 16 s 11 s 11 s 30s 21 s 21 s 38 s 28 s 28 s
GASSST 110 s 58 s 42 s 216 s 116 s 78 s 268 s 145 s 96 s
BWA 64 s 34 s 22 s 150 s 88 s 54 s 214 s 104 s 71 s
Speedup1 6.8 5.3 3.8 7.2 5.5 3.7 7.1 5.2 3.4
Speedup2 4 3.1 2.0 5.0 4.2 2.6 5.7 3.7 2.5

(Note: speedup1 indicates the runtime comparison between the hybrid system and GASSST; speedup2 indicates the execution time comparison between the hybrid system and BWA).

Chen et al.

Chen et al. BMC Bioinformatics 2013 14:67   doi:10.1186/1471-2105-14-67

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