Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin
- PMID: 29773078
- PMCID: PMC5956843
- DOI: 10.1186/s40168-018-0470-z
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin
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.
Conflict of interest statement
Ethics approval and consent to participate
Not applicable
Competing interests
The authors declare that they have no competing interests.
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Figures
![Fig. 1](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/5956843/bin/40168_2018_470_Fig1_HTML.gif)
![Fig. 2](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/5956843/bin/40168_2018_470_Fig2_HTML.gif)
![Fig. 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/5956843/bin/40168_2018_470_Fig3_HTML.gif)
![Fig. 4](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/5956843/bin/40168_2018_470_Fig4_HTML.gif)
![Fig. 5](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/5956843/bin/40168_2018_470_Fig5_HTML.gif)
Similar articles
-
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.Microbiome. 2020 Aug 28;8(1):124. doi: 10.1186/s40168-020-00900-2. Microbiome. 2020. PMID: 32859275 Free PMC article.
-
Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data.Indian J Med Res. 2020 Jan;151(1):93-103. doi: 10.4103/ijmr.IJMR_220_18. Indian J Med Res. 2020. PMID: 32134020 Free PMC article.
-
IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.Microbiome. 2018 Aug 9;6(1):140. doi: 10.1186/s40168-018-0521-5. Microbiome. 2018. PMID: 30092815 Free PMC article.
-
A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.BMC Bioinformatics. 2017 May 10;18(1):247. doi: 10.1186/s12859-017-1670-4. BMC Bioinformatics. 2017. PMID: 28486927 Free PMC article.
-
Mycofier: a new machine learning-based classifier for fungal ITS sequences.BMC Res Notes. 2016 Aug 11;9(1):402. doi: 10.1186/s13104-016-2203-3. BMC Res Notes. 2016. PMID: 27516337 Free PMC article.
Cited by
-
Dysbiosis not observed in Canadian horse with free fecal liquid (FFL) using 16S rRNA sequencing.Sci Rep. 2024 Jun 5;14(1):12903. doi: 10.1038/s41598-024-63868-1. Sci Rep. 2024. PMID: 38839848 Free PMC article.
-
Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border.Sci Rep. 2024 Jun 4;14(1):12803. doi: 10.1038/s41598-024-63356-6. Sci Rep. 2024. PMID: 38834753 Free PMC article.
-
Gut microbiome in the Graves' disease: Comparison before and after anti-thyroid drug treatment.PLoS One. 2024 May 31;19(5):e0300678. doi: 10.1371/journal.pone.0300678. eCollection 2024. PLoS One. 2024. PMID: 38820506 Free PMC article.
-
Th17-to-Tfh plasticity during periodontitis limits disease pathology.J Exp Med. 2024 Aug 5;221(8):e20232015. doi: 10.1084/jem.20232015. Epub 2024 May 31. J Exp Med. 2024. PMID: 38819409 Free PMC article.
-
Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems.mLife. 2022 Nov 3;1(4):399-411. doi: 10.1002/mlf2.12042. eCollection 2022 Dec. mLife. 2022. PMID: 38818486 Free PMC article.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical
Research Materials
Miscellaneous