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Table 3 Performance of GPU-based implementations on real datasets

From: GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

  Throughput (GCUPS) GPU (sec) CPU (sec) Speedup
Stage 1 of S2 1.86 2.32 43.93 18.94x
Stage 2 of S2 - 0.14 0.62 4.43x
Overall of S2 - 3.15 44.55 14.14x
Stage 1 of S3 0.64 10.20 53.29 5.22x
Stage 2 of S3 - 0.09 0.17 1.89x
Overall of S3 - 10.93 53.46 4.89x
  1. S2 and S3 stand for situation 2 and 3, respectively. “Overall of S2” and “Overall of S3” represent the overall GPU execution time? CPU execution time and speedup of situation 2 and 3, respectively