Table 1

k-mer statistics.

Correction tool

Running time

k-mers

Reads


Total

Genomic

Non-genomic

% of all genomic k-mers found in reads

% genomic among all k-mers in reads

% reads aligned to genome


Multi-cell E. coli, total 4,543,849 genomic k-mers


Uncorrected

187,580,875

4,543,684

183,037,191

99.99

2.4

99.05

Quake

4,565,237

4,543,461

21,776

99.99

99.5

99.97

HammerNoExpansion

30 m

58,305,738

4,543,674

53,762,064

99.99

8.4

95.59

HammerExpanded

36 m

28,290,788

4,543,673

23,747,115

99.99

19.1

99.49

BayesHammer

37 m

27,100,305

4,543,674

22,556,631

99.99

20.1

99.62


Single-cell E. coli, total 4,543,849 genomic k-mers


Uncorrected

165,355,467

4,450,489

160,904,978

97.9

2.7

79.05

Camel

2 h 29 m

147,297,070

4,450,311

142,846,759

97.9

3.0

81.25

Euler-SR

2 h 15 m

138,677,818

4,450,431

134,227,387

97.9

3.2

81.95

Coral

2 h 47 m

156,907,496

4,449,560

152,457,936

97.9

2.8

80.28

HammerNoExpansion

37 m

53,001,778

4,443,538

48,558,240

97.8

8.3

81.36

HammerExpanded

43 m

36,471,268

4,443,545

32,027,723

97.8

12.1

86.91

BayesHammer

57 m

35,862,329

4,443,736

31,418,593

97.8

12.4

87.12


Single-cell S. aureus, total 2,821,095 genomic k-mers


Uncorrected

88,331,311

2,820,394

85,510,917

99.98

3.2

75.07

Camel

5 h 13 m

69,365,311

2,820,350

66,544,961

99.97

4.1

75.27

Euler-SR

2 h 33 m

58,886,372

2,820,349

56,066,023

99.97

4.8

75.24

Coral

7 h 12 m

83,249,146

2,820,011

80,429,135

99.96

3.4

75.22

HammerNoExpansion

58 m

37,465,296

2,820,341

34,644,955

99.97

7.5

71.63

HammerExpanded

1 h 03 m

23,197,521

2,820,316

20,377,205

99.97

12.1

76.54

BayesHammer

1 h 09 m

22,457,509

2,820,311

19,637,198

99.97

12.6

76.60


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

Open Data