Table 1 Comparison of WHATSHAP POLYPHASE and H-POPG on tetraploid real (a) and simulated (b) datasets, pentaploid simulated dataset (c), and hexaploid simulated dataset (d). Performances are based on the switch error rate (SER), block-wise Hamming rate (HR), and N50 for the block size. For better comparability with H-POPG, a second setting (WH-PP*) with less block cuts was used. The total length of the chromosome is 249 Mb

(a) Real tetraploid read data

40 ×

WH-PP

0.58

1.48

29,529

3333

1.41

WH-PP*

1.39

28.72

1,692,352

3433

1.42

H-PoPG

2.01

27.53

1,785,293

2230

9.97

80 ×

WH-PP

0.31

1.43

54,434

12694

2.52

WH-PP*

0.74

28.27

2,587,104

13042

2.89

H-PoPG

1.24

27.66

2,587,104

4368

9.99

(b) Simulated tetraploid read data

40 ×

WH-PP

0.42

1.74

48,815

1960

1.10

WH-PP*

1.00

26.57

1,830,943

2004

1.17

H-PoPG

1.67

26.37

1,917,094

1414

9.96

80 ×

WH-PP

0.29

2.51

86,227

5738

1.78

WH-PP*

0.68

25.23

2,142,893

5865

2.04

H-PoPG

0.98

25.65

2,142,893

2843

9.97

(c) Simulated pentaploid read data

40 ×

WH-PP

0.86

1.57

22,625

2331

1.05

WH-PP*

2.01

25.34

1,361,459

2377

1.07

H-PoPG

3.50

24.78

1,453,040

2357

9.97

80 ×

WH-PP

0.47

1.18

33,438

5031

1.69

WH-PP*

1.33

23.64

1,701,753

5118

1.87

H-PoPG

2.24

24.76

1,748,404

4849

9.96

(d) Simulated hexaploid read data

40 ×

WH-PP

1.12

1.82

16,785

25841

1.30

WH-PP*

2.35

27.03

3,877,456

25860

1.79

H-PoPG

3.85

26.75

4,490,129

5450

9.96

80 ×

WH-PP

0.48

0.97

26,711

10331

1.98

WH-PP*

1.34

25.63

4,540,968

10827

2.63

H-PoPG

2.37

25.93

4,721,421

11563

10.89