Table 2. Comparison of MICCA, QIIME and UPARSE on both 16-10 and ITS-10 datasets in terms of average % of reads passing the quality filtering step, number of OTUs found, chimeric and redundant OTUs (i.e. OTUs corresponding to the same centroid in the synthetic datasets). Standard deviations are indicated in parentheses.

Dataset	Pipeline	% reads passing the filtering step	OTUs found	% Chimeric Reads	Chimeric OTUs	Redundant OTUs
16S-10	MICCA	86.6 (1.8)	173.4 (6.2)	13.1 (0.7)	0.5 (0.5)	0 (0)
	QIIME	84.4 (2.1)	263.3 (9.6)	12.0 (0.6)	26.8 (5.8)	31.5 (3.4)
	UPARSE	64.6 (2.4)	148.3 (7.4)	15.5 (0.8)	0.2 (0.4)	0 (0)
ITS-10	MICCA	74.1 (5.2)	93 (2.3)	12.7 (0.5)	0.6 (0.8)	0 (0)
	QIIME	71.8 (5.5)	179.1 (7.5)	11.5 (0.5)	28.7 (10.4)	34 (2.3)
	UPARSE	66.8 (4.1)	89.5 (1.8)	15.5 (0.6)	0.1 (0.3)	0.9 (0.7)