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Table 1 Evaluation of Hifiasm assembly, Trio assembly, Hifiasm + Hi-C assembly and gcaPDA assembly

From: gcaPDA: a haplotype-resolved diploid assembler

Assembly

Contigs

k-mer completeness (%)

Gene completeness (%)

Total (Mb)

No

N50 (Mb)

All

Hap SK

Hap B73

PPV*

Comp

Dup

Frag

Mis

Reference

SK

2154

671

223.2

76.15

100.00

0.00

NA

96.1

6.0

1.3

2.6

B73

2104

267

220.8

75.97

0.00

100.00

NA

95.5

6.1

1.5

3.0

B73 + SK

4258

938

223.2

100.00

100.00

100.00

NA

96.9

94.8

0.9

2.2

Hifiasm

Hap1

2160

800

77.3

75.69

54.91

48.75

53.16

94.4

8.6

1.0

4.6

Hap2

2160

673

72.4

75.89

48.47

55.35

53.12

95.2

8.3

0.8

4.0

Hap1 + Hap2

4319

1473

75.5

99.86

99.75

99.67

53.14

97.6

94.2

0.2

2.2

Hifiasm + Hi-C

HapSK

2134

671

96.9

75.98

97.53

2.49

97.53

96.4

5.3

0.9

2.7

HapB73

2124

690

48.0

76.02

2.81

97.76

97.18

96.1

5.8

1.2

2.7

HapSK + hapB73

4258

1361

69.6

99.96

99.89

99.93

97.36

97.7

94.9

0.2

2.1

Trio

HapSK

2160

1118

60.0

76.06

99.62

0.58

99.43

96.1

7.6

0.8

2.7

HapB73

2118

811

35.6

75.98

0.49

99.85

99.51

96.5

7.2

1.2

2.9

HapSK + hapB73

4278

1929

44.9

99.90

99.65

99.92

99.47

97.8

94.9

0.4

2.1

gcaPDA

HapSK

2162

767

55.3

76.19

98.87

1.78

98.25

95.9

6.5

1.4

2.7

HapB73

2159

699

57.0

76.41

2.25

99.46

97.77

95.4

6.2

1.6

3.0

HapSK + hapB73

4320

1466

55.3

99.67

99.06

99.56

98.01

96.9

94.5

1.0

2.2

  1. *PPV indicates positive predictive value