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Table 1 Performance comparison of AltHap, H-PoP, BP, HapTree, SCGD, and ILP applied to haplotype reconstruction of the CEU NA12878 data set in the 1000 Genomes Project

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

97.4

2011

11.26

95.7

2264

5.22

99.1

2321

8.17

2

95.3

2562

12.22

95.6

2971

5.65

89.5

2897

9.83

3

93.3

2084

10.38

91.2

2312

6.99

74.3

2367

8.30

4

96.9

2368

12.16

97.0

2648

5.24

74.8

2613

6.76

5

97.2

1924

9.96

96.6

2103

4.67

88.2

2185

4.76

6

94.9

3687

14.17

95.2

3343

4.93

88.7

3588

6.94

7

97.0

1846

11.19

92.4

1986

4.24

81.1

2073

7.88

8

96.2

1634

9.63

94.7

1848

4.14

88.5

1857

8.01

9

97.1

1272

6.42

91.0

1462

3.36

89.8

1491

6.13

10

96.8

1584

7.97

94.5

1683

3.67

90.8

1839

7.18

11

93.3

1394

7.45

91.5

1553

3.71

75.6

1586

6.69

12

92.1

1423

7.12

90.3

1570

3.46

74.4

1589

6.48

13

97.0

1269

4.42

94.1

1440

2.89

89.1

1409

5.38

14

90.3

857

9.53

97.1

974

2.54

70.0

995

4.53

15

97.2

941

9.42

97.4

1039

2.40

74.6

1063

3.92

16

96.7

1198

5.40

93.5

1192

2.47

79.7

1269

4.42

17

97.5

1146

4.58

91.1

1244

1.98

92.4

1234

3.15

18

91.0

860

4.54

97.6

893

2.51

82.0

942

3.79

19

97.6

618

3.32

97.8

695

1.82

98.0

1060

2.47

20

97.3

703

3.53

95.0

719

2.00

97.1

796

2.74

21

97.4

470

2.51

97.0

512

1.70

97.5

532

1.86

22

97.3

367

1.98

98.3

427

1.44

90.7

438

1.72

Mean

95.8

1464

7.69

94.8

1585

3.50

85.0

1643

5.51

Sd

2.27

780

3.54

2.54

790

1.49

8.94

793

2.32

# best

9

0

0

5

0

5

3

0

0

 

HapTree

SCGD

ILP

Chromosome

CPR

MEC

t(sec)

CPR

MEC

t(sec)

CPR

MEC

t(sec)

1

84.1

2305

15.43

92.5

2456

3.62

95.6

1741

173.68

2

84.5

2875

17.59

92.6

3509

4.41

95.3

2219

190.37

3

85.2

2363

15.06

91.9

2498

3.40

95.6

1788

152.09

4

83.5

2604

18.67

92.7

3754

5.47

97.1

2048

168.56

5

84.8

2171

16.95

93.9

2750

3.54

95.4

1691

147.72

6

84.6

3583

23.86

93.0

5612

8.70

95.7

2643

181.51

7

84.7

2070

13.06

93.5

2826

3.95

95.4

1590

133.36

8

84.2

1838

14.81

90.7

1692

2.18

95.6

1472

136.60

9

85.1

1479

14.90

97.1

1885

2.94

95.2

1125

105.34

10

85.7

1823

12.13

92.6

1876

2.56

95.7

1354

120.89

11

83.6

1577

11.33

93.2

2265

2.95

95.2

1206

104.74

12

84.8

1589

9.97

92.3

1612

2.03

95.4

1214

103.88

13

82.8

1405

9.55

97.0

2947

3.31

95.5

1105

93.33

14

85.4

987

7.79

91.1

904

1.36

95.3

752

65.07

15

83.6

1061

7.43

99.1

1041

1.21

94.1

809

66.52

16

85.1

1273

8.13

93.0

1305

1.79

95.5

920

77.81

17

84.8

1230

6.34

96.7

2123

2.61

96.1

943

47.99

18

84.1

941

7.13

90.3

933

1.16

95.2

720

71.49

19

84.6

765

5.26

97.2

1290

3.25

96.6

533

44.32

20

86.9

795

6.08

96.8

949

1.38

95.8

612

54.30

21

86.3

528

5.05

94.3

499

0.63

95.2

415

31.82

22

86.9

436

4.65

94.1

422

0.74

95.2

316

31.89

Mean

84.8

1623

11.42

93.9

2052

2.87

95.5

1237

104.69

Sd

1.03

802

5.23

2.3

1222

1.80

0.57

612

50.37

# best

0

0

0

1

0

17

5

22

0

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