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Table 2 Comparative statistics for the assembly and scaffolding of Synechococcus sp. WH8103, Rhodobacter sphaeroides and Homo sapiens Chr.14

From: WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

  

Synechococcus sp. WH8103

Rhodobacter sphaeroides

Homo sapiens Chr.14

  

CONTIGS

SCAFFOLDS

CONTIGS

SCAFFOLDS

CONTIGS

SCAFFOLDS

Contiguity Statistics

Assembler/Scaffolder

CLC

WISCA

SSPACE

SOPRA

SCARPA

CLC

Bambus2

WISCA

SSPACE

SOPRA

SCARPA

CABOG

WISCA

SSPACE

SOPRA

SCARPA

Number of scaffolds

n.a.

3

13

5

7

36

n.a.

17

116

18

30

n.a.

228

930

414

259

Unscaffolded contigs

42

13

n.a.

22

23

n.a.

177

33

n.a.

136

39

3,541

184

n.a.

2,587

468

Fragmentsa ≥ 10 kbp

17

3

4

8

15

13

72

16

59

64

34

2,132

221

435

1,885

362

Max. scaffold size (kbp)

357

1,296

889

779

357

500

279

2,502

279

407

1,346

297

2,554

1,592

497

2,253

N50b (kbp)

211

1,296

729

367

222

278

97

2,502

134

118

178

47

694

348

56

499

LG50c

5

1

2

3

5

4

17

1

13

14

5

563

38

74

460

52

LG75c

8

2

3

5

8

6

38

5

27

31

13

1,217

79

161

1,008

115

Nb of Ns (kbp)

n.a.

2.4

10.2

7.8

15.0

20.0

n.a.

8.9

35.0

11.0

55.6

n.a.

178.7

359.3

38.0

304.8

Genome coverage (%)d

98.72

98.86

98.92

98.72

98.72

98.80

94.97

94.97

95.06

94.97

94.77

97.70

97.73

97.69

97.70

97.35

Misassembliesh

Misassemblies

0

13

2

2

5

2

4

62

7

6

10

108

981

177

120

200

-Relocationse

0

11

2

2

5

2

1

48

3

2

6

106

743

175

118

199

-Translocationsf

0

0

0

0

0

0

3

8

4

4

4

0

0

0

0

0

-Inversionsg

0

2

0

0

0

0

0

6

0

0

0

2

238

2

2

1

Misassembled contigs

0

2

1

1

3

2

4

10

6

6

7

87

177

105

96

101

Local misassemblies

11

28

36

22

12

19

308

365

352

324

369

454

1,932

2,125

668

1,368

Mismatches

2

7

20

2

7

34

254

287

279

268

280

87,135

86,626

86,856

87,335

85,748

Indels

0

3

1

3

1

3

255

277

273

267

270

19,990

20,656

20,740

20,511

21,102

-short indels

0

1

0

1

1

2

195

204

206

202

203

17,000

16,912

17,126

17,190

17,333

-long indels

0

2

1

2

0

1

60

73

67

65

67

2,990

3,744

3,614

3,321

3,769

Indels length

0

19

15

55

3

38

2,035

2,423

2,223

2,124

2,230

72,044

103,854

92,992

80,016

92,442

  1. n.a. not applicable, WISCA WiseScaffolder, ai.e. scaffolds and unscaffolded contigs; bcontig size over which the sum of contig sizes corresponds to 50 % of the assembly; cminimal number of fragments (contigs/scaffold) to cover 50 %/75 % of the reference genome; dcalculated as \( \frac{\varSigma \kern0.5em contigs\kern0.5em length-\kern0.5em Nb\kern0.5em of\kern0.5em Ns}{\operatorname{Reference}\kern0.5em genome\kern0.5em length}\times 100 \); emisassembly where contiguous sequence fragments align on the same chromosome but where the left sequence fragment aligns over 1 kbp away from the right sequence fragment on the reference or overlap by more than 1 kbp; fmisassembly where the sequence fragments align on different chromosomes; gmisassembly where the sequence fragments align on opposite strands of the same chromosome; hmisassembly statistics are results from QUAST [15]
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BMC Bioinformatics

ISSN: 1471-2105

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