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Table 1 Classification speed of CLARK, Kraken, and cuCLARK at species-level measured in terms of 106 classified sequences (reads) per minute

From: Accelerating metagenomic read classification on CUDA-enabled GPUs

 

CPU threads

GPUs

HiSeq Speed

MiSeq Speed

wgsim200 Speed

wgsim250 Speed

art454 Speed

fqIon Speed

CLARK

1

-

1.89

0.88

0.68

0.54

0.29

0.74

CLARK

16

-

15.74

9.74

8.15

6.82

4.05

9.47

Kraken

1

-

2.37

1.33

1.15

0.89

0.64

1.32

Kraken

16

-

12.6

13.74

14.45

11.95

8.75

15.48

cuCLARK

8

1

49.69

42.27

38.02

34.5

26.84

41.01

cuCLARK/CLARK

  

3.2

4.3

4.7

5.1

6.6

4.3

cuCLARK/Kraken

  

3.9

3.1

2.6

2.9

3.1

2.7

  1. The bottom two rows report the speedups between cuCLARK over CLARK and Kraken executed with 16 CPU threads