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Table 1 Number of taxonomic groups identified by each classifier among Illumina 16S rRNA gene sequences (SRR3225706) from a mock microbiome sample [33]. Counts are provided with and without including any sequences in the RDP training set that are labeled as belonging to the 20 expected genera

From: IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

   Classified to genus levelα (%) Groups present in the mock community Absent from mock communityβ
Root Domain Phylum Class Order Family Genus Order Family Genus
Using the RDP training set BLAST 97.9 1 0 0 0 0 0 17 0 0 24
IDTAXA 94.2 1 0 1 1 2 5 14 0 1 2
MAPSeq 96.5 1 0 0 0 0 4 15 0 2 6
QIIME 95.4 1 0 0 0 0 0 16 0 0 7
RDP Classifier 93.3 1 1 2 3 6 8 15 0 2 6
SINTAX 94.2 1 1 1 4 3 3 14 1 0 3
SPINGO 96.5 1 0 0 0 0 0 17 0 0 3
With expected genera excluded from training data BLAST 17.3 1 0 0 0 0 0 0 0 0 65
IDTAXA 0.01 1 1 1 2 3 4 0 0 2 2
MAPSeq 24.6 1 0 0 2 5 11 0 1 8 20
QIIME 13.5 1 0 0 0 0 0 0 0 0 16
RDP Classifier 3.83 1 1 2 3 6 9 0 0 3 12
SINTAX 8.76 1 1 1 7 5 6 0 1 1 9
SPINGO 26.7 1 0 0 0 0 0 0 0 0 15
  1. αPercent of total sequences from the mock community that were classified to the genus rank
  2. βOther rank levels (root, domain, phylum, and class) all had counts of zero