Table 1 Statistics of the quantitative evaluation of the BioMaS, QIIME and Mothur pipelines
From: BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS
a) Illumina bacteria test case | ||||||||||||
BioMaS | QIIME | Mothur | ||||||||||
Rank | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR |
Kingdom | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
Phylum | 100.00 | 100.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 | 44.47 | 100.00 | 0.00 | 55.53 |
Class | 100.00 | 100.00 | 0.00 | 0.00 | 100.00 | 100.00 | 0.00 | 0.00 | 44.35 | 100.00 | 0.00 | 55.65 |
Order | 97.62 | 99.98 | 0.02 | 2.38 | 97.62 | 99.98 | 0.02 | 2.38 | 39.13 | 100.00 | 0.00 | 60.87 |
Family | 94.23 | 99.96 | 0.04 | 5.77 | 94.23 | 99.96 | 0.04 | 5.77 | 36.50 | 99.98 | 0.02 | 63.50 |
Genus | 87.00 | 99.90 | 0.10 | 13.00 | 66.03 | 99.91 | 0.09 | 33.97 | 16.91 | 99.89 | 0.11 | 83.09 |
Species | 87.28 | 99.92 | 0.08 | 12.72 | 28.13 | 99.95 | 0.05 | 71.87 | 9.38 | 99.73 | 0.27 | 90.63 |
b) Roche 454 bacteria test case | ||||||||||||
BioMaS | QIIME | Mothur | ||||||||||
Rank | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR |
Kingdom | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
Phylum | 99.99 | 100.00 | 0.00 | 0.01 | 99.23 | 100.00 | 0.00 | 0.77 | 35.63 | 99.99 | 0.01 | 64.37 |
Class | 99.99 | 100.00 | 0.00 | 0.01 | 96.26 | 100.00 | 0.00 | 0.89 | 34.20 | 99.99 | 0.01 | 65.80 |
Order | 97.61 | 99.99 | 0.01 | 2.39 | 94.16 | 99.98 | 0.02 | 3.46 | 29.98 | 99.99 | 0.01 | 70.02 |
Family | 91.80 | 99.98 | 0.02 | 6.27 | 87.49 | 99.97 | 0.03 | 8.66 | 26.61 | 99.98 | 0.02 | 71.46 |
Genus | 82.14 | 99.94 | 0.06 | 16.32 | 68.53 | 99.94 | 0.06 | 28.40 | 11.94 | 99.91 | 0.09 | 86.52 |
Species | 68.88 | 99.96 | 0.04 | 24.87 | 42.58 | 99.88 | 0.12 | 51.17 | 8.81 | 99.80 | 0.20 | 84.94 |
c) Illumina fungi test case | ||||||||||||
BioMaS | QIIME | Mothur | ||||||||||
Rank | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR |
Kingdom | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
Phylum | 100.00 | 100.00 | 0.00 | 0.00 | 97.15 | 99.51 | 0.49 | 2.85 | 99.51 | 100.00 | 0.00 | 0.49 |
Class | 99.73 | 100.00 | 0.00 | 0.27 | 72.77 | 99.36 | 0.64 | 27.23 | 92.09 | 99.76 | 0.24 | 7.91 |
Order | 96.30 | 100.00 | 0.00 | 3.70 | 65.15 | 99.66 | 0.34 | 24.85 | 85.92 | 99.90 | 0.10 | 14.08 |
Family | 93.20 | 100.00 | 0.00 | 6.80 | 66.36 | 99.23 | 0.77 | 25.64 | 84.28 | 99.94 | 0.06 | 15.72 |
Genus | 94.47 | 99.92 | 0.08 | 5.53 | 65.50 | 99.67 | 0.33 | 24.98 | 75.07 | 99.84 | 0.16 | 23.34 |
Species | 83.55 | 99.90 | 0.10 | 16.45 | 30.69 | 99.35 | 0.65 | 57.43 | 53.74 | 99.79 | 0.21 | 44.28 |
d) Roche 454 fungi test case | ||||||||||||
BioMaS | QIIME | Mothur | ||||||||||
Rank | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR | TPR | TNR | FPR | FNR |
Kingdom | 100.00 | 0.00 | 0.00 | 0.00 | 99.10 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
Phylum | 98.64 | 100.00 | 0.00 | 1.36 | 97.96 | 99.89 | 0.11 | 2.04 | 99.10 | 100.00 | 0.00 | 0.90 |
Class | 99.44 | 100.00 | 0.00 | 0.56 | 72.12 | 99.76 | 0.24 | 27.88 | 93.72 | 99.92 | 0.08 | 6.28 |
Order | 96.35 | 100.00 | 0.00 | 3.65 | 56.27 | 99.82 | 0.18 | 20.40 | 83.79 | 99.97 | 0.03 | 16.21 |
Family | 92.79 | 100.00 | 0.00 | 7.21 | 56.00 | 99.62 | 0.38 | 22.00 | 84.43 | 99.98 | 0.02 | 15.57 |
Genus | 94.44 | 99.97 | 0.03 | 5.56 | 57.18 | 99.86 | 0.14 | 17.42 | 75.60 | 99.93 | 0.07 | 24.40 |
Species | 89.25 | 99.96 | 0.04 | 10.75 | 33.75 | 99.84 | 0.16 | 41.50 | 53.24 | 99.92 | 0.08 | 46.76 |