دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.
المؤلفون: Bokulich NA; The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA. nicholas.bokulich@nau.edu., Kaehler BD; Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton ACT, 2601, Australia. benjamin.kaehler@anu.edu.au., Rideout JR; The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA., Dillon M; The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA., Bolyen E; The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA., Knight R; Departments of Pediatrics and Computer Science and Engineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Huttley GA; Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton ACT, 2601, Australia. gavin.huttley@anu.edu.au., Gregory Caporaso J; The Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ, 86011-4073, USA. gregcaporaso@gmail.com.; Department of Biological Sciences, Northern Arizona University, 1298 S Knoles Drive, Building 56, 3rd Floor, Flagstaff, AZ, USA. gregcaporaso@gmail.com.
المصدر: Microbiome [Microbiome] 2018 May 17; Vol. 6 (1), pp. 90. Date of Electronic Publication: 2018 May 17.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101615147 Publication Model: Electronic Cited Medium: Internet ISSN: 2049-2618 (Electronic) Linking ISSN: 20492618 NLM ISO Abbreviation: Microbiome Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London: BioMed Central, 2013-
مواضيع طبية MeSH: Computer Simulation*, Bacteria/*genetics , DNA, Intergenic/*genetics , Fungi/*genetics , Microbiota/*genetics , RNA, Ribosomal, 16S/*genetics , Sequence Alignment/*methods, Algorithms ; Base Sequence/genetics ; Machine Learning ; Software
مستخلص: 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.
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معلومات مُعتمدة: U54 CA143924 United States CA NCI NIH HHS; U54 CA143925 United States CA NCI NIH HHS
المشرفين على المادة: 0 (DNA, Intergenic)
0 (RNA, Ribosomal, 16S)
تواريخ الأحداث: Date Created: 20180519 Date Completed: 20190111 Latest Revision: 20221017
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC5956843
DOI: 10.1186/s40168-018-0470-z
PMID: 29773078
قاعدة البيانات: MEDLINE
الوصف
تدمد:2049-2618
DOI:10.1186/s40168-018-0470-z