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Table 2 Performance comparison of AltHap, H-PoP, BP, HapTree, SCGD, and ILP applied to the Fosmid data set. HapTree could not finish assembling haplotype of the 6th chromosome in 48 hours

From: Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids

 

AltHap

H-PoP

BP

Chromosome

CPR

MEC

t(sec)

CPR

MEC

t(sec)

CPR

MEC

t(sec)

1

95.5

9731

18.38

84.8

9845

2.13

87.6

9567

40.18

2

95.5

9589

38.89

90.4

9444

2.16

84.8

9698

42.90

3

91.7

7311

29.40

91.7

7182

1.79

84.7

7587

30.61

4

92.7

5508

26.69

92.6

5775

1.76

86.9

6288

31.10

5

92.0

6711

27.39

93.9

6910

1.95

86.3

6975

36.94

6

90.9

7213

33.68

88.5

7505

2.40

85.0

7590

41.20

7

90.7

6151

28.60

91.9

6829

1.68

85.8

6091

36.94

8

91.2

5927

23.82

90.2

6143

1.89

87.3

6282

38.87

9

91.8

5347

19.40

91.8

5719

1.76

85.1

5493

26.13

10

90.1

6044

24.07

92.4

6328

1.48

86.4

6503

27.65

11

90.8

5424

21.73

90.3

6432

1.68

85.8

5579

20.56

12

91.5

5456

24.25

91.4

5653

1.46

85.0

5706

24.19

13

90.4

3646

14.23

90.1

3708

1.54

82.7

3976

17.33

14

89.5

4156

18.64

89.1

4261

1.21

87.0

4004

14.84

15

90.0

4079

14.67

72.9

4001

1.06

82.3

4022

14.35

16

88.5

6197

26.28

71.5

6119

1.20

84.4

5112

29.51

17

89.7

4507

16.35

88.3

4911

1.22

87.6

4749

18.29

18

93.0

3080

12.68

90.8

3315

1.14

85.5

3457

13.31

19

85.7

4212

13.40

86.3

4115

0.84

83.5

3928

13.44

20

90.3

3512

13.64

90.0

4121

0.85

84.9

3814

15.97

21

92.7

1871

6.20

91.9

1974

0.68

87.2

1953

8.18

22

85.1

3654

17.24

87.8

3757

0.62

86.7

3910

14.72

mean

90.9

5424

21.35

88.6

5639

1.48

85.6

5558

25.33

Sd

2.5

1950

7.79

5.7

1934

0.50

1.5

1948

10.84

# best

13

0

0

4

0

9

0

0

0

 

HapTree

SCGD

ILP

Chromosome

CPR

MEC

t(sec)

CPR

MEC

t(sec)

CPR

MEC

t(sec)

1

91.5

9676

6501

95.1

10127

2.59

79.0

6889

80.33

2

92.3

9802

7196

94.5

9721

2.41

76.1

6700

76.60

3

90.7

7705

4847

88.6

7410

1.83

76.9

5122

79.50

4

90.8

6500

8392

87.6

5494

1.48

77.0

4072

51.49

5

90.8

7094

5670

89.6

7058

1.71

76.0

4637

54.39

6

-

-

-

90.4

7843

2.14

75.7

5248

63.37

7

91.5

6169

5589

89.4

6189

1.73

77.9

4174

46.85

8

91.2

6379

8316

87.4

5996

1.47

76.3

4301

53.57

9

91.7

5513

4465

90.0

5592

1.20

76.8

3974

42.41

10

88.9

6553

4838

92.8

6027

1.60

76.8

4508

59.25

11

90.5

5625

5183

90.1

5662

1.34

79.0

3903

45.45

12

91.3

5770

5654

90.5

5731

1.55

77.5

3907

48.76

13

89.8

4029

5367

87.6

3727

0.79

77.1

2669

32.09

14

90.6

4038

4103

92.9

4859

1.12

75.4

2814

39.61

15

90.7

4116

3357

87.8

4442

0.88

78.7

2903

33.80

16

94.2

5142

9683

95.5

6474

1.60

79.8

3844

62.44

17

93.1

4806

3003

97.1

4843

1.01

80.8

3448

42.00

18

91.9

3493

2303

88.3

3478

0.71

76.9

2337

32.27

19

92.8

3953

1984

82.5

4204

0.87

78.6

2707

33.68

20

90.1

3886

1529

94.6

3790

0.83

78.7

2783

31.78

21

92.1

1979

1410

90.7

2042

0.36

77.2

1367

16.42

22

92.4

3307

1351

90.6

3495

1.06

77.0

2422

60.62

mean

91.4

5502

4797.19

90.6

5645

1.38

77.6

3851

49.39

Sd

1.2

1998

2392.54

3.4

1977

0.56

1.39

1360

16.82

# best

4

0

0

4

0

13

0

22

0

  1. The best results in each Chromosome and in all Chromosomes are in bolface font