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Table 1 Average speedup of CES over NPS for all PaCo tasks taking on average at least 15 min

From: Impact of concurrency on the performance of a whole exome sequencing pipeline

Task

4 processors

8 processors

16 processors

Mean ± Std (s)

Mean ± Std (s)

Mean ± Std (s)

(a) 2-samples execution

 Align to nuclear

1.75 ± 0.01

2.84 ± 0.02

3.19 ± 0.04

 Align to exome

1.76 ± 0.01

1.79 ± 0.01

2.87 ± 0.07

 Identify INDELs nuclear

1.95 ± 0.01

1.83 ± 0.01

2.15 ± 0.09

 Compute BQSR nuclear

2.38 ± 0.03

2.69 ± 0.02

2.91 ± 0.15

 Post BQSR nuclear

3.09 ± 0.01

3.17 ± 0.03

3.1 ± 0.04

Task

6 processors

12 processors

24 processors

Mean ± Std (s)

Mean ± Std (s)

Mean ± Std (s)

(b) 3-samples execution.

 Align to nuclear

2.05 ± 0.01

3.72 ± 0.01

3.91 ± 0.05

 Align to exome

1.61 ± 0.01

2.06 ± 0.01

3.62 ± 0.05

 Identify INDELs nuclear

1.88 ± 0.03

2.2 ± 0.06

2.75 ± 0.16

 Compute BQSR nuclear

2.96 ± 0.02

3.26 ± 0.03

3.96 ± 0.14

 Post BQSR nuclear

4.32 ± 0.03

4.37 ± 0.12

4.43 ± 0.04

  1. Number of processors stands for the number of available processors managed by both strategies