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Table 3 Performance of PMFFRC on S. fontinalis 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

5.33

–

0.76

–

0.67

2.05

0.45

2.24

-u20, k3

3.49

34.52

0.50

52.48

11.90

1.75

5.22

3.05

-u40, k1

3.41

36.02

0.48

56.22

23.69

2.04

6.71

3.78

SPRING

Without

5.49

–

0.78

–

1.02

1.46

0.56

0.29

-u20, k3

3.58

34.79

0.51

50.38

12.76

1.74

1.49

0.59

-u40, k1

3.49

36.43

0.49

57.45

25.51

1.69

1.53

0.91

Mstcom

Without

3.87

–

0.55

–

5.91

7.19

2.29

1.06

-u40, k6

2.40

37.98

0.34

64.31

33.24

5.09

20.03

0.76

-u100, k3

2.31

40.31

0.33

67.93

78.97

5.47

50.36

1.11

-u180, k1

2.26

41.60

0.32

71.12

159.13

6.22

100.72

1.60

FastqCLS

Without

4.37

–

0.62

–

16.66

21.51

6.35

16.25

-u80, k4

2.82

35.47

0.40

55.15

60.36

11.66

6.38

14.44

-u180, k3

2.77

36.61

0.39

58.00

59.09

12.98

6.43

14.04

-u280, k1

2.69

38.44

0.38

62.56

63.60

14.03

6.39

15.95

  1. Parameters: Pr = 20, T = 8, βHARC = 1.05, βSPRING = 0.95, 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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