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Table 2 Evaluation summary of HG002 assemblies

From: Accurate long-read de novo assembly evaluation with Inspector

Assembly

 

Contig continuity

 

Assembly error

 

QUAST-LG

 

Merqury

 

Reference-based mode

 

# Contig

Total

Max

N50

 

Structural

Small-scale

QV

 

Misassembly

MM

 

QV

 

NA50

MR (%)

Coverage (%)

CLR

 

Canu

 

4751

2.91

72.0

7.2

 

103

39.82

43.63

 

8341

18.84

 

38.51

 

1.32

99.15

89.41

 

Flye

 

2168

2.82

66.6

12.0

 

192

30.88

43.38

 

4005

16.46

 

38.71

 

1.47

99.36

88.67

 

Wtdbg2

 

2947

2.77

48.5

7.0

 

158

430.00

33.46

 

8943

29.13

 

29.42

 

0.43

97.77

86.17

HiFi

 

Canu

 

1376

3.37

192.2

65.3

 

5

1.90

54.85

 

47672

29.17

 

46.57

 

2.20

95.95

91.71

 

Flye

 

2379

2.96

136.6

35.1

 

256

20.74

43.69

 

14478

17.34

 

48.08

 

2.28

97.82

90.36

 

wtdbg2

 

1652

2.76

74.8

16.3

 

251

83.06

39.42

 

4124

14.65

 

42.66

 

1.56

99.38

86.77

 

hifiasm

 

559

3.07

199.4

111.1

 

18

3.62

53.62

 

31143

21.47

 

45.88

 

2.53

97.37

92.03

Nanopore

 

Canu

 

745

2.90

101.3

33.1

 

1432

3845.99

24.05

 

14926

100.03

 

22.94

 

0.27

98.27

88.46

 

Flye

 

584

2.87

109.9

51.7

 

481

316.46

34.30

 

7688

33.94

 

30.46

 

1.48

99.32

89.80

 

wtdbg2

 

7959

2.97

54.2

8.2

 

2226

2116.76

24.91

 

23159

65.88

 

24.49

 

0.30

93.79

84.91

 

Shasta

 

1258

2.80

129.3

23.3

 

2527

2554.72

25.74

 

9063

70.15

 

24.76

 

0.31

99.16

87.71

  1. The unit of Max, N50, and NA50 is Mbp. The unit of Total is Gbp. The unit of small-scale and MM is per Mbp. Misassembly of QUAST-LG includes both extensive and local misassembly. Mismatch of QUAST-LG includes both mismatches and indels
  2. Total total number of bases, Max length of the longest contig, MM number of mismatches, MR mapping ratio of assembled contigs