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Table 2 Comparison of clustering methods based on Smith-Waterman alignment scores

From: Rapid analysis of metagenomic data using signature-based clustering

Wound Microbiome

46313157 sequences, average sequence length: 337

Method

Time

Clusters

Intercluster

 

Intracluster

 
 

(m)

 

Avg

SD

Avg

SD

SigClust

16

5254

59.0

58.7

234.4

97.9

Merged SigClust

18

1260

55.5

51.2

211.6

104.9

UClust T=0.75

156

7141

50.3

41.8

202.9

95.0

16S Genus

2586

2221

43.9

28.0

188.9

92.5

16S Species

2586

8375

48.7

39.6

205.8

93.6

16S Strains

2586

9354

50.1

42.6

206.7

93.5

Oral Metagenome – Human (mgp41)[11]

1237319 sequences, average sequence length: 59

Method

Time

Clusters

Intercluster

 

Intracluster

 
 

(m)

 

Avg

SD

Avg

SD

SigClust

0.2

17621

25.5

11.8

53.7

9.6

UClust T=0.75

1.7

17621

20.2

6.9

43.4

9.1

PRJEB4688 [12]

5497442 sequences, average sequence length: 253

Method

Time

Clusters

Intercluster

 

Intracluster

 
 

(m)

 

Avg

SD

Avg

SD

SigClust

1.62

6998

44.4

48.5

257.7

67.0

UClust T=0.75

9

6998

37.1

38.0

159.1

66.9

  1. As before, results are shown for the wound data, and for two previously published Illumina metagenomic datasets. We report for each method the clustering time in minutes and the number of clusters returned. The remaining columns of the table show the mean and standard deviation of the separation for the sampled intercluster and intracluster pairs