Table 1.

Benchmarking of DADA2, deblur and CDSnake on three mock community datasets and set of these datasets, where each mock dataset represented one sample (All row)

	actual number of microbial strains	pipeline	OTUs/Features outputted	OTUs/Features annotated	OTUs/Features correctly annotated	Microorganisms correctly discovered	Total count
Balanced	59	dada2	91	67	57	39	29,344
		deblur	343	280	244	41	200,317
		CDSnake	55	45	31	29	524,604
HMP	21	dada2	68	49	31	19	186,027
		deblur	53	36	23	18	175,027
		CDSnake	59	21	17	17	214,831
Extreme	27	dada2	30	26	25	18	1,371,591
		deblur	18	15	14	13	775,144
		CDSnake	12	12	9	8	1,357,589
All	~ 105	dada2	180	134	116	77	1,392,444
		deblur	393	317	274	68	224,388
		CDSnake	123	31	26	25	2,231,154