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Table 1 Number of OTUs and species diversity estimation by LSH-Div algorithm.

From: 16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing

OTUs Cutoff Distance 0.03

Sample

Reads

# OTUs

Chao1

HI

ACE

53R

11218

1459

3726.53

4.59

3564.58

55R

8680

1461

3915.25

4.92

4274.4

112R

11132

2111

6838.9

5.62

7255.16

115R

13441

1540

3930.08

4.6

3972.27

137

12259

1266

3181.92

4.85

2740.44

138

11554

1306

3031.06

4.61

2998.51

FS312

52569

4321

13942.28

4.78

14345.15

FS396

73657

4594

14228.93

4.18

14826.74

OTUs Cutoff Distance 0.05

53R

11218

1172

3050.32

4.22

2786.32

55R

8680

1199

3296.38

4.53

3531.21

112R

11132

1795

5781.85

5.19

6126.08

115R

13441

1205

3042.52

4.25

3094.09

137

12259

1041

2595.72

4.60

2317.95

138

11554

1072

2351.90

4.28

2372.84

FS312

52569

3505

10367.35

4.56

10353.72

FS396

73657

3676

10672.02

4.04

10579.55

OTUs Cutoff Distance 0.10

53R

11218

914

2308.14

3.95

2154.07

55R

8680

963

2418.55

4.35

2538.92

112R

11132

1506

4787.73

4.96

5040.54

115R

13441

943

2446.11

3.83

2409.63

137

12259

817

2028.76

4.24

1831.79

138

11554

845

1985.47

4.02

1827.27

FS312

52569

2771

7038.76

4.22

7444.19

FS396

73657

2876

7534.98

3.84

7370.95

  1. Several species diversity metrics and number of OTUs produced by LSH-Div algorithm on samples taken from Sogin et. al. [27]. The experiment uses three OTU definitions 0.03, 0.05, and 0.10 which define the cutoff levels in distance units. OTU denotes the number of OTUs observed, Chao1 denotes the Chao1 estimate, H´ denotes the Shannon diversity index and ACE denotes the Abundance-based Coverage Estimator. The parameter setting used by LSH-Div algorithm to obtain these results is k = 30, w-mer = 3.
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BMC Systems Biology

ISSN: 1752-0509

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