Microbial taxonomy 
sintax commandnbc_tax command
Recommended taxonomy reference databases
Sequence databases with taxonomy annotations
Taxonomic nomenclatures (naming systems)
Defining taxa
TAXXI benchmark
SILVA and Greengenes "taxonomies"
Phylogenetic consistency in microbial taxonomy
Confidence values for taxonomy predictions
References (please cite)
R.C. Edgar (2016), SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, https://doi.org/10.1101/074161
• SINTAX taxonomy prediction algorithm
• Fast and simple method, accuracy comparable to RDP Classifier
R.C. Edgar (2018), Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences, PeerJ 6:e4652
• Cross-validation by identity, novel benchmark strategy enabling realistic accuracy estimates
• Genus accuracy of best methods is 50% on V4 sequences
• Recent algorithms do not improve on RDP Classifier or SINTAX
R.C. Edgar (2018), Taxonomy annotation and guide tree errors in 16S rRNA databases, PeerJ 6:e5030
• Approx. one in five SILVA and Greengenes taxonomy annotations are wrong
• SILVA and Greengenes trees have pervasive conflicts with type strain taxonomies
