CONSTAX2: improved taxonomic classification of environmental DNA markers
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 implementationCONSTAX2 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 informationSupplementary data are available at Bioinformatics online.
- Research Organization:
- Michigan State University, East Lansing, MI (United States); University of Wisconsin, Madison, WI (United States)
- Sponsoring Organization:
- National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Grant/Contract Number:
- SC0018409
- OSTI ID:
- 1829161
- Alternate ID(s):
- OSTI ID: 1979482
- Journal Information:
- Bioinformatics, Journal Name: Bioinformatics Journal Issue: 21 Vol. 37; ISSN 1367-4803
- Publisher:
- Oxford University PressCopyright Statement
- Country of Publication:
- United Kingdom
- Language:
- English