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.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 data are available at Bioinformatics online.
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Related Subject Headings
- Software
- Eukaryota
- Documentation
- DNA, Environmental
- Bioinformatics
- Algorithms
- 49 Mathematical sciences
- 46 Information and computing sciences
- 31 Biological sciences
- 08 Information and Computing Sciences
Citation
Published In
DOI
EISSN
ISSN
Publication Date
Volume
Issue
Start / End Page
Related Subject Headings
- Software
- Eukaryota
- Documentation
- DNA, Environmental
- Bioinformatics
- Algorithms
- 49 Mathematical sciences
- 46 Information and computing sciences
- 31 Biological sciences
- 08 Information and Computing Sciences