Table 1 Comparison of clustering methods based on Needleman-Wunsch alignment scores
From: Rapid analysis of metagenomic data using signature-based clustering
Wound Microbiome | ||||||
46313157 sequences, average sequence length: 337 | ||||||
Method | Time | Clusters | Intercluster | Â | Intracluster | |
| Â | (m) | Â | Avg | SD | Avg | SD |
SigClust | 16 | 5254 | -68.8 | 125.1 | 219.4 | 107.7 |
Merged SigClust | 18 | 1260 | -73.9 | 118.0 | 180.9 | 136.9 |
UClust T=0.75 | 156 | 7141 | -81.4 | 111.6 | 148.5 | 142.1 |
16S Genus | 2586 | 2221 | -82.4 | 104.6 | 98.6 | 167.4 |
16S Species | 2586 | 8375 | -76.9 | 110.8 | 125.6 | 162.5 |
16S Strains | 2586 | 9354 | -82.4 | 104.6 | 98.6 | 167.4 |
Oral Metagenome – Human (mgp41)[11] | ||||||
1237319 sequences, average sequence length: 59 | ||||||
Method | Time | Clusters | Intercluster | Â | Intracluster | |
| Â | (m) | Â | Avg | SD | Avg | SD |
SigClust | 0.2 | 17621 | 5.5 | 22.3 | 51.6 | 14.1 |
UClust T=0.75 | 1.7 | 17621 | -4.4 | 14.4 | 38.8 | 13.3 |
PRJEB4688 [12] | ||||||
5497442 sequences, average sequence length: 253 | ||||||
Method | Time | Clusters | Intercluster | Â | Intracluster | |
| Â | (m) | Â | Avg | SD | Avg | SD |
SigClust | 1.62 | 6998 | -94.8 | 126.6 | 250.1 | 77.2 |
UClust T=0.75 | 9 | 6998 | -109.0 | 117.4 | 121.5 | 93.5 |