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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