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Table 2 Assembly metrics after MaGuS scaffolding for the five assemblies

From: MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

 

SOAP

SSPACE

SGA

BESST

OPERA-LG

Assembly size (bp)

115 563 956

116 414 299

115 703 449

115 174 685

116 556 828

N50 (bp)

1 350 715

1 680 424

635 106

1 751 177

1 442 963

N50 fold change

1.64

1.74

2.24

1.35

1.13

L50

23

18

47

18

22

N75 (bp)

509 384

646 442

288 240

787 050

695 198

N75 fold change

1.66

1.9

2.43

1.22

1.23

L75

58

48

110

42

51

Number of N's per 100 kb

4 055.34

3 331.14

4 869.38

2 995.68

3 264.70

Largest alignment

5 012 555

7 708 756

3 361 051

6 902 343

5 597 743

NA50

1 187 620

1 455 792

579 394

1 407 579

1 258 868

NA50 fold change

1.57

1.57

2.1

1.16

1.18

NA75

354 088

508 625

215 751

609 320

560 902

NA75 fold change

1.32

1.75

2.15

1.18

1.59

Total misassemblies

23

19

19

36

62

Magus misassemblies

14

10

16

13

5

Number of map-links

534

481

1 034

371

368

Number of MP-validated links

209 (39.14 %)

214 (44.49 %)

516 (49.9 %)

93 (25.07 %)

78 (21.2 %)

Number of correct MP-validated links

195 (36.51 %)

204 (42.41 %)

500 (48.53 %)

80 (21.56 %)

73 (19.83 %)

False positive rate

6.7

4.7

3.1

14

6.4