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Table 3 Results of RIEMS validation using the Clinical PathoScope simulated sample dataset

From: RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Input species True positive False positive True negative False negative Unclassified Sensitivity Specificity Positive predictive value Negative predicitive value Correct classification rate False classification rate
Haemophilus influenzae 344646 17 9643530 7010 3 98.01 100 100 99.93 99.93 0.07
Homo sapiens 8975152 8541 986662 24848 7 99.72 99.14 99.9 97.54 99.67 0.33
Human mastadenovirus B 59289 0 9931563 4351 0 93.16 100 100 99.96 99.96 0.04
Human bocavirus 9 0 9995193 1 0 90 100 100 100 100 0
Human coronavirus NL63 24375 0 9970203 625 5 97.5 100 100 99.99 99.99 0.01
Enterovirus A 911 0 9994203 89 0 91.1 100 100 100 100 0
Human respiratory syncytial virus 9855 0 9985203 145 56 98.55 100 100 100 100 0
Rhinovirus C 241 0 9994953 9 0 96.4 100 100 100 100 0
Influenza A virus 15 0 9995103 85 0 15 100 100 100 100 0
Moraxella catarrhalis 169607 7 9823264 2325 1 98.65 100 100 99.98 99.98 0.02
Streptococcus pneumoniae 193919 18 9800120 1146 0 99.41 100 99.99 99.99 99.99 0.01
Streptococcus intermedius 175739 47 9818606 811 0 99.54 100 99.97 99.99 99.99 0.01