Table 6 Assembling the corrected reads using Canu. Assess the influence of different correction methods for diploid/polyploid genome assembly. In the completeness (%) multicolumn, all is the k-mer completeness for both haplotypes combined, matis maternal hap-mer completeness and pat is paternal hap-mer completeness. Switch error rate = the ratio of the number of switches between true and alternative haplotypes to the total number of variant positions

Arabidopsis thaliana

     Canu

Ratatosk

22.87

0.52

66.55

40.31

40.31

8.59

     Canu

R-HERO

23.86

0.41

70.13

43.05

43.05

7.94

     Canu

FMLRC

23.63

0.43

61.46

32.51

32.29

11.34

     Canu

F-HERO

23.88

0.41

61.89

33.01

32.10

11.17

     Canu

LoRDEC

25.15

0.31

48.22

25.64

26.15

12.18

     Canu

L-HERO

25.61

0.27

58.23

32.35

32.38

11.05

Oryza sativa japonica

     Canu

Ratatosk

25.23

0.30

50.36

—

—

—

     Canu

R-HERO

28.40

0.14

58.87

—

—

—

     Canu

FMLRC

25.75

0.27

28.36

—

—

—

     Canu

F-HERO

29.53

0.11

34.33

—

—

—

     Canu

LoRDEC

25.88

0.26

30.28

—

—

—

     Canu

L-HERO

29.83

0.10

54.27

—

—

—

Oryza sativa aromatic

     Canu

Ratatosk

24.12

0.39

12.32

—

—

—

     Canu

R-HERO

29.03

0.13

58.89

—

—

—

     Canu

FMLRC

30.17

0.10

1.15

—

—

—

     Canu

F-HERO

32.63

0.05

3.57

—

—

—

     Canu

LoRDEC

25.76

0.27

4.38

—

—

—

     Canu

L-HERO

29.94

0.10

41.28

—

—

—

Mangifera indica

     Canu

Ratatosk

24.44

0.36

90.60

—

—

—

     Canu

R-HERO

26.41

0.23

90.43

—

—

—

     Canu

FMLRC

28.48

0.14

75.22

—

—

—

     Canu

F-HERO

30.05

0.10

75.19

—

—

—

     Canu

LoRDEC

24.67

0.34

61.46

—

—

—

     Canu

L-HERO

26.88

0.21

70.09

—

—

—