Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities

Table 2 Genus Level Classification

Pipeline	OTU Strategy	OTU algorithm	Reference	Undercalled (%)	Undercalled (Ranks off)	Correct (%)	Misscalled (%)	Miscalled (Ranks off)	Lost (%)
QIIME	Closed		GreenGenes	24.0	1 (1–3)	53.7	19.3	4 (1–9)	3.0
QIIME	Sub	UClust	GreenGenes	27.8	1 (1–3)	50.4	21.6	4 (1–9)	0.2
QIIME	Sub	UClust	Silva	11.6	1 (1–5)	74.8	13.4	4 (1–13)	0.2
QIIME	De novo	UClust	GreenGenes	22.9	1 (1–3)	53.5	23.5	4 (1–9)	0.1
QIIME	De novo	UClust	Silva	12.0	1 (1–3)	74.6	13.3	4 (1–11)	0.1
QIIME	De novo	Swarm	GreenGenes	26.3	1 (1–3)	50.5	23.1	5 (1–9)	0.1
MOTHUR	Closed		Silva/RDP	5	1 (1–2)	56.5	21.9	9 (1–11)	16.6
pplacer	De novo	Swarm	RDP	31.7	2 (1–7)	55.2	11.9	4 (1–9)	1.2

Summary of Classification Performance. On the left are the various conditions tested. The first column specifies the pipeline, the second the OTU strategy, the third the methodological details (e.g. reference set or algorithm used). Table 1 is for species-level classification, Table 2 is for genus-level. Source organisms can be correctly called, undercalled (in the correct clade, but not the target species or genus level classification), or miscalled (placed down the wrong taxonomic clade). We present both the percentage in each category (correct, undercalled, and miscalled) and the median (min and max parenthetical) taxonomic ranks off for underacalled and miscalled source organisms

ISSN: 1471-2105