Table 6

Accuracy of 3% OTU construction following application of the noise removal algorithms

Name

AmpliconNoise

SLP 1%

SLP 2%

DeNoiser


3% OTUs

Good

Missed

Noise

Good

Missed

Noise

Good

Missed

Noise

Good

Missed

Noise


Divergent

26

0

1

26

1

162

26

1

11

24

0

3

Artificial

34

0

1

38

0

109

32

2

10

36

0

6

Even1

57

0

131

60

2

174

39

19

65

59

1

21

Even2

57

0

89

59

2

137

42

15

53

58

3

22

Even3

58

0

125

65

0

197

43

17

75

58

3

23

Uneven1

58

0

101

60

0

144

47

10

59

54

7

24

Uneven2

48

0

35

51

0

74

38

10

26

46

6

6

Uneven3

49

1

46

51

2

97

41

10

45

48

6

12


Titanium


σs = 0.1

66

0

8

74

0

169

67

1

18

15

53

14

σs = 0.04

67

0

21


Reads classified as chimeric by comparison with the references were removed prior to complete linkage OTU construction at 3% sequence difference with the corresponding reference sequences. Each OTU was then classified as 'Good' if it comprised reference sequences and denoised pyrosequenced reads, 'Missed' OTUs are formed only from reference sequences, and those OTUs containing only pyrosequenced reads are designated 'Noise'. The numbers of classified OTUs observed for each data set and noise removal algorithm are shown below.

Quince et al. BMC Bioinformatics 2011 12:38   doi:10.1186/1471-2105-12-38

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