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Microbial taxonomy

  sintax command
  nbc_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