Skip to main content

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
  1. Average True Positive Rate (TPR), average True Negative Rate (TNR), average False Positive Rate (FPR) and average False Negative Rate (FNR) values for all the considered ranks (from kingdom to species) are shown for BioMaS, QIIME and Mothur computation. The table is divided in 4 sections, as follows: a) Illumina Bacteria test case, b) Roche 454 Bacteria test case, c) Illumina Fungi test case, and d) Roche 454 Fungi test case.