CONSTAX2: Improved taxonomic classification of environmental DNA markers.

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: 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.