CONSTAX2: improved taxonomic classification of environmental DNA markers
Abstract
Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States); Michigan State Univ., East Lansing, MI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1829161
- Alternate Identifier(s):
- OSTI ID: 1979482
- Grant/Contract Number:
- SC0018409; DEB 1737898
- Resource Type:
- Published Article
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Name: Bioinformatics Journal Volume: 37 Journal Issue: 21; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Liber, Julian A., Bonito, Gregory, Benucci, Gian Maria Niccolò, and Marschall, ed., Tobias. CONSTAX2: improved taxonomic classification of environmental DNA markers. United Kingdom: N. p., 2021.
Web. doi:10.1093/bioinformatics/btab347.
Liber, Julian A., Bonito, Gregory, Benucci, Gian Maria Niccolò, & Marschall, ed., Tobias. CONSTAX2: improved taxonomic classification of environmental DNA markers. United Kingdom. https://doi.org/10.1093/bioinformatics/btab347
Liber, Julian A., Bonito, Gregory, Benucci, Gian Maria Niccolò, and Marschall, ed., Tobias. Fri .
"CONSTAX2: improved taxonomic classification of environmental DNA markers". United Kingdom. https://doi.org/10.1093/bioinformatics/btab347.
@article{osti_1829161,
title = {CONSTAX2: improved taxonomic classification of environmental DNA markers},
author = {Liber, Julian A. and Bonito, Gregory and Benucci, Gian Maria Niccolò and Marschall, ed., Tobias},
abstractNote = {Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/btab347},
journal = {Bioinformatics},
number = 21,
volume = 37,
place = {United Kingdom},
year = {Fri May 07 00:00:00 EDT 2021},
month = {Fri May 07 00:00:00 EDT 2021}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/bioinformatics/btab347
https://doi.org/10.1093/bioinformatics/btab347
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
journal, December 2017
- Gdanetz, Kristi; Benucci, Gian Maria Niccolò; Vande Pol, Natalie
- BMC Bioinformatics, Vol. 18, Issue 1
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007
- Wang, Q.; Garrity, G. M.; Tiedje, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 16
Bioconda: sustainable and comprehensive software distribution for the life sciences
journal, July 2018
- Grüning, Björn; Dale, Ryan; Sjödin, Andreas
- Nature Methods, Vol. 15, Issue 7
High throughput sequencing methods and analysis for microbiome research
journal, December 2013
- Di Bella, Julia M.; Bao, Yige; Gloor, Gregory B.
- Journal of Microbiological Methods, Vol. 95, Issue 3
Improved metagenomic analysis with Kraken 2
journal, November 2019
- Wood, Derrick E.; Lu, Jennifer; Langmead, Ben
- Genome Biology, Vol. 20, Issue 1
SPINGO: a rapid species-classifier for microbial amplicon sequences
journal, October 2015
- Allard, Guy; Ryan, Feargal J.; Jeffery, Ian B.
- BMC Bioinformatics, Vol. 16, Issue 1
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
journal, October 2018
- Nilsson, Rolf Henrik; Larsson, Karl-Henrik; Taylor, Andy F. S.
- Nucleic Acids Research, Vol. 47, Issue D1
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
journal, May 2018
- Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout, Jai Ram
- Microbiome, Vol. 6, Issue 1
Scraping the bottom of the barrel: are rare high throughput sequences artifacts?
journal, February 2015
- Brown, Shawn P.; Veach, Allison M.; Rigdon-Huss, Anne R.
- Fungal Ecology, Vol. 13
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
25 years of serving the community with ribosomal RNA gene reference databases and tools
journal, November 2017
- Glöckner, Frank Oliver; Yilmaz, Pelin; Quast, Christian
- Journal of Biotechnology, Vol. 261
Improved tools for biological sequence comparison.
journal, April 1988
- Pearson, W. R.; Lipman, D. J.
- Proceedings of the National Academy of Sciences, Vol. 85, Issue 8, p. 2444-2448
UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013
- Edgar, Robert C.
- Nature Methods, Vol. 10, Issue 10