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 | |