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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
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BMC Genomics

ISSN: 1471-2164

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