Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, James G Caporaso

Research output: Contribution to journalArticle

141 Scopus citations

Abstract

Background: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. Results: We present q2-feature-classifier (https://github.com/qiime2/q2-feature-classifier), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data. The naive-Bayes, BLAST+-based, and VSEARCH-based classifiers implemented in QIIME 2 meet or exceed the species-level accuracy of other commonly used methods designed for classification of marker gene sequences that were evaluated in this work. These evaluations, based on 19 mock communities and error-free sequence simulations, including classification of simulated "novel" marker-gene sequences, are available in our extensible benchmarking framework, tax-credit (https://github.com/caporaso-lab/tax-credit-data). Conclusions: Our results illustrate the importance of parameter tuning for optimizing classifier performance, and we make recommendations regarding parameter choices for these classifiers under a range of standard operating conditions. q2-feature-classifier and tax-credit are both free, open-source, BSD-licensed packages available on GitHub.

Original languageEnglish (US)
Article number90
JournalMicrobiome
Volume6
Issue number1
DOIs
StatePublished - May 17 2018

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ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Bokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M., Bolyen, E., Knight, R., Huttley, G. A., & Caporaso, J. G. (2018). Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome, 6(1), [90]. https://doi.org/10.1186/s40168-018-0470-z