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

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

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

ISSN: 1471-2105