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Table 4 Performance of PMFFRC on C. arietinum dataset

From: PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering

Algorithm

Parameter

Compression

Decompression

cs (GB)

pss (%)

cr (bits/base)

crg (%)

cpm (GB)

ct (h)

dpm (GB)

dt (h)

HARC

Without

16.96

–

0.79

–

1.99

5.24

1.74

6.14

-u20, k5

11.17

34.14

0.52

51.85

17.75

3.05

6.30

6.60

-u40, k3

10.95

35.44

0.51

51.94

34.73

3.16

7.11

7.60

-u80, k1

10.78

36.44

0.50

58.90

66.90

3.53

6.97

5.05

SPRING

Without

15.82

–

0.73

–

1.89

5.73

1.04

0.66

-u20, k5

11.05

30.15

0.51

43.15

18.91

3.55

2.93

0.95

-u40, k3

10.87

31.29

0.50

43.54

36.78

3.60

4.09

1.02

-u100, k1

10.67

32.55

0.49

48.29

70.79

4.09

4.13

1.19

Mstcom

Without

13.01

–

0.60

–

14.54

66.52

6.49

2.94

-u100, k15

10.34

20.52

0.48

25.88

37.52

64.52

22.45

2.31

-u200, k7

9.59

26.29

0.44

35.71

77.51

61.85

50.98

2.29

-u300, k4

9.24

28.98

0.43

40.91

149.86

59.62

102.78

2.15

FastqCLS

Without

27.62

–

1.28

–

33.79

50.36

6.49

28.84

-u100, k9

25.08

9.20

1.16

10.15

36.30

28.13

6.56

23.88

-u200, k5

23.65

14.37

1.10

16.81

36.01

30.76

6.53

22.16

-u300, k4

22.88

17.16

1.06

20.76

35.84

30.32

6.55

22.42

  1. Parameters: Pr = 20, T = 8, βHARC = 1.05, βSPRING = 0.30, βFastqCLS = 0.28, βMstcom = 0.75, x1 = 100, x2 = 100,100. The compression gains obtained by the PMFFRC cascaded algorithms is marked in boldface. “–” means the result of not being optimized by the PMFFRC algorithm
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BMC Bioinformatics

ISSN: 1471-2105

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