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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