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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.