Table 2

Assembly results, single-cell E.coli and S. aureus datasets (contigs of length ≥ 200 are used).

Statistics

BayesHammer

BayesHammer(scaff old)

Coral

Coral (scaff old)

EulerSR

EulerSR (scaff old)

Hammer, expanded

Hammer, no expansion

Hammer, no expansion(scaff old)

Hammer(scaff old)


Single-cell E. coli, reference length 4639675, reference GC content 50.79%


# contigs (1000 bp)

191

158

276

224

231

150

195

282

242

173

# contigs

521

462

675

592

578

375

529

655

592

477

Largest contig

269177

284968

179022

179022

267676

267676

268464

210850

210850

268464

Total length

4952297

4989404

5064570

4817757

4817757

4902434

4977294

5097148

5340871

5005022

N50

110539

113056

45672

67849

74139

95704

97639

65415

84893

109826

NG50

112065

118432

55073

87317

77762

108976

101871

68595

96600

112161

NA50

110539

113056

45672

67765

74139

95704

97639

65415

84841

109826

NGA50

112064

118432

55073

87317

77762

108976

101871

68594

96361

112161

# misassemblies

4

6

9

12

6

8

4

4

7

7

# misassembled contigs

4

6

9

10

6

8

4

4

7

7

Misass. contigs length

42496

94172

62114

150232

47372

149639

43304

26872

147140

130706

Genome covered (%)

96.320

96.315

96.623

96.646

95.337

95.231

96.287

96.247

96.228

96.281

GC (%)

49.70

49.69

49.61

49.56

49.90

49.74

49.68

49.64

49.60

49.68

# mismatches/100 kbp

11.22

11.70

8.36

9.10

5.55

5.82

12.77

54.11

52.48

13.08

# indels/100 kbp

1.07

8.26

9.17

12.76

0.52

47.80

0.91

1.17

7.96

8.69

# genes

4065 +

4079 +

3998 +

4040 +

3992 +

4020 +

4068 +

4034 +

4048 +

4078 +

124 part

110 part

180 part

143 part

140 part

107 part

123 part

152 part

136 part

111 part


Single-cell S. aureus, reference length 2872769, reference GC content 32.75%


# contigs (1000 bp)

95

85

132

113

82

70

114

272

258

101

Total length (1000 bp)

3019597

3309342

3055585

3066662

2972925

2993100

3033912

3389846

3405223

3509555

# contigs

260

241

455

423

166

134

312

721

711

292

Largest contig

282558

328686

208166

208166

254085

535477

282558

148002

166053

328679

Total length

3081173

3368034

3160497

3166169

3008746

3020256

3111423

3575679

3594468

3584266

N50

87684

145466

62429

90701

101836

145466

74715

30788

34943

131272

NG50

112566

194902

87636

99341

108151

159555

88292

39768

45889

180022

NA50

87684

145466

62429

89365

100509

145466

68711

30788

34552

112801

NGA50

88246

148064

74452

90101

101836

145466

88289

35998

42642

148023

# misassemblies

15

17

11

14

4

5

11

14

18

14

# misassembled contigs

12

14

9

10

4

5

9

14

16

12

Misass. contigs length

340603

779785

478009

523596

377133

918380

402997

272677

324361

940356

Genome covered (%)

99.522

99.483

99.449

99.447

99.213

99.254

99.204

98.820

98.888

99.221

GC (%)

32.67

32.63

32.64

32.63

32.66

32.67

32.67

32.39

32.38

32.57

# mismatches per 100 kbp

3.18

8.01

12.44

12.65

9.72

10.28

17.38

54.92

55.50

15.36

# indels per 100 kbp

2.17

2.30

15.50

15.67

3.80

4.08

3.57

2.64

2.72

3.04

# genes

2540 +

2547 +

2532 +

2540 +

2547 +

2550 +

2535 +

2477 +

2485 +

2539 +

36 part

30 part

45 part

37 part

30 part

27 part

41 part

91 part

85 part

38 part


Nikolenko et al. BMC Genomics 2013 14(Suppl 1):S7   doi:10.1186/1471-2164-14-S1-S7

Open Data