Journal
MICROBIOME
Volume 6, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s40168-018-0470-z
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Funding
- National Science Foundation [1565100]
- Alfred P. Sloan Foundation
- Partnership for Native American Cancer Prevention (NIH/NCI) [U54CA143924, U54CA143925]
- National Health and Medical Research Council of Australia [APP1085372]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1565100] Funding Source: National Science Foundation
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Background: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. Results: We present q2-feature-classifier (https://github.corn/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.comkaporaso 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.
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