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

Microbiome
Nicholas A BokulichJ Gregory Caporaso

Abstract

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. 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 ). Our results illustrate the i...Continue Reading

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Citations

Sep 29, 2018·Genes·Tasha M Santiago-Rodriguez, Gary A Toranzos
Apr 27, 2019·Environmental Microbiology·Jason A RothmanQuinn S McFrederick
Mar 29, 2019·The British Journal of Dermatology·C Hidalgo-CantabranaP Coto-Segura
Jul 26, 2019·FEMS Microbiology Ecology·Giulia AlessandriMarco Ventura
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Nov 12, 2019·Environmental Microbiology·Katarina DamjanovicMadeleine J H van Oppen
Oct 6, 2019·Applied and Environmental Microbiology·Angela Peña-GonzalezKonstantinos T Konstantinidis
Nov 7, 2019·Global Change Biology·Homère J Alves MonteiroJérémy Le Luyer
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Methods Mentioned

BETA
PCR
profilers
feature extraction

Software Mentioned

RDP
Mock
uclust
QIIME1
legacy
learn
SortMeRNA
Linux
Greengenes
mockrobiota

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