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 language | English (US) |
|---|---|
| Article number | 90 |
| Journal | Microbiome |
| Volume | 6 |
| Issue number | 1 |
| DOIs | |
| State | Published - May 17 2018 |
Fingerprint
ASJC Scopus subject areas
- Microbiology
- Microbiology (medical)
Cite this
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. / Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout, Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob; Huttley, Gavin A.; Caporaso, James G.
In: Microbiome, Vol. 6, No. 1, 90, 17.05.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin
AU - Bokulich, Nicholas A.
AU - Kaehler, Benjamin D.
AU - Rideout, Jai Ram
AU - Dillon, Matthew
AU - Bolyen, Evan
AU - Knight, Rob
AU - Huttley, Gavin A.
AU - Caporaso, James G
PY - 2018/5/17
Y1 - 2018/5/17
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85052651259&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85052651259&partnerID=8YFLogxK
U2 - 10.1186/s40168-018-0470-z
DO - 10.1186/s40168-018-0470-z
M3 - Article
VL - 6
JO - Microbiome
JF - Microbiome
SN - 2049-2618
IS - 1
M1 - 90
ER -