From: Environmental metagenome classification for constructing a microbiome fingerprint
 |  | AKL | HAM | NYC | OFA | PXO | SAC | SCL | TOK | Total |
---|---|---|---|---|---|---|---|---|---|---|
Ryan [21] | #correct | 7 | 10 | 25 | 20 | 60 | 16 | 18 | 20 | \(\sum =176\) |
 | PPV | 0.54 | 0.56 | 0.96 | 0.95 | 0.98 | 1 | 1 | 1 | Ns=193 |
 | TPR | 0.47 | 0.63 | 0.96 | 1 | 1 | 1 | 0.9 | 1 | ACC=0.912 |
Sanchez et al. [24] | #correct | 9 | 11 | 110 | 17 | 60 | 34 | 17 | 20 | \({\sum }=278\) |
 | PPV | 0.69 | 0.73 | 0.95 | 0.89 | 1 | 0.83 | 0.89 | 0.71 | Ns=311 |
 | TPR | 0.6 | 0.69 | 0.87 | 0.85 | 1 | 1 | 0.85 | 1 | ACC=0.894 |
Harris et al. [32] | — | — | — | — | — | — | — | — | — | Ns=N/A |
 |  |  |  |  |  |  |  |  |  | ACC=0.897 |
Walker and Datta [22] | TPR (median) | 0.6 | 0.62 | 0.58 | 0.95 | 0.87 | 0.76 | 0.3 | 0.7 | Ns=211 |
 | — | — | — | — | — | — | — | — | — | ACC=0.71 |
Zhu [25] | #correct | 5 | 3 | 114 | 14 | 51 | 31 | 17 | 15 | \({\sum }=250\) |
 | TPR | 0.33 | 0.19 | 0.9 | 0.74 | 0.85 | 0.91 | 0.85 | 0.75 | Ns=310 |
 |  |  |  |  |  |  |  |  |  | ACC=0.81 |
Chierici et al. [23] | — | — | — | — | — | — | — | — | — | Ns=311 |
 |  |  |  |  |  |  |  |  |  | ACC=0.894 |
Our method using Mash | #correct | 15 | 15 | 50 | 20 | 60 | 31 | 19 | 20 | \({\sum }=230\) |
sketch size=1000 | PPV | 0.34 | 0.26 | 1.00 | 0.67 | 1.00 | 1.00 | 1.00 | 1.00 | Ns=311 |
 | TPR | 1.00 | 0.94 | 0.40 | 1.00 | 1.00 | 0.91 | 0.95 | 1.00 | ACC=0.740 |
Our method using Mash | #correct | 15 | 16 | 42 | 20 | 60 | 34 | 20 | 20 | \({\sum }=227\) |
sketch size=10000 | PPV | 0.65 | 0.18 | 1.00 | 0.83 | 1.00 | 1.00 | 1.00 | 1.00 | Ns=311 |
 | TPR | 1.00 | 1.00 | 0.33 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | ACC=0.730 |
Our method using Mash | #correct | 15 | 16 | 44 | 20 | 60 | 34 | 19 | 20 | \({\sum }=228\) |
sketch size=100000 | PPV | 0.60 | 0.18 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | Ns=311 |
 | TPR | 1.00 | 1.00 | 0.35 | 1.00 | 1.00 | 1.00 | 0.95 | 1.00 | ACC=0.733 |
Our method using CoMeta | #correct | 4 | 12 | 116 | 20 | 37 | 34 | 13 | 20 | \({\sum }=256\) |
(class-level filtering) | PPV | 0.67 | 0.63 | 0.92 | 0.74 | 1.00 | 0.97 | 1 | 0.42 | Ns=311 |
 | TPR | 0.27 | 0.75 | 0.92 | 1.00 | 0.62 | 1.00 | 0.65 | 1.00 | ACC=0.823 |
Our method using CoMeta | #correct | 4 | 13 | 113 | 20 | 57 | 30 | 16 | 19 | \({\sum }=272\) |
(sample-level filtering) | PPV | 0.57 | 0.65 | 0.92 | 0.65 | 0.92 | 1.00 | 0.94 | 0.9 | Ns=311 |
 | TPR | 0.27 | 0.81 | 0.9 | 1.00 | 0.95 | 0.88 | 0.8 | 0.95 | ACC=0.875 |