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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)

From: CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities

  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