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Table 1 Accuracy test

From: Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

 

60 seqs

50 × 60 seqs

Reference expected values

59

57

52

59

57

52

CROP

59

59

59

60

60

60

ESPRIT

59

57

52

59

57

52

MAFFT+JC

58

56

50

58

57

51

MAFFT+MAFFT

59

59

59

59

59

59

MAFFT+Mothur

59

56

51

59

57

54

Mothur+JC

55

55

55

2992

2992

2992

Mothur+MAFFT

41

40

36

252

251

243

Mothur+Mothur

48

48

48

48

48

48

Mothur+PreC+JC

44

44

44

43

43

43

Mothur+PreC+MAFFT

47

47

47

47

47

47

Mothur+PreC+Mothur

48

48

48

48

48

48

MUSCLE+JC

58

56

50

63

59

59

MUSCLE+MAFFT

59

59

59

59

59

59

MUSCLE+Mothur

59

56

55

66

62

56

Otupipe

59

57

52

59

57

52

RDP

59

57

52

59

57

52

  1. OTUs observed with each of the workflows analysed at distances of 3, 5 and 10% for the datasets containing 60 test sequences and 50 replicas of the same (50 × 60). JC stands for Jukes-Cantor and PreC for the pre-clustering step applied after Mothur MSA. Combined workflows are indicated stating first the method used for alignment (MAFFT, Mucle, Mothur or Mothur with pre-clustering), and then the distance method used (Jukes-Cantor, MAFFT or Mothur). Clustering was performed with Mothur for all combined workflows.
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BMC Bioinformatics

ISSN: 1471-2105

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