HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.

Motivation: Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining the functional roles of microbial communities. A key challenge in analyzing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxa of origin. While still performing worse relative to reference-based short-read tools in species classification, ML algorithms have shown promising results in taxonomic classification at higher ranks. A recent approach exploited to enhance the performance of ML tools, which can be translated to reference-dependent classifiers, has been to integrate the hierarchical structure of taxonomy within the tool's predictive algorithm. Results: Here, we introduce HiTaxon, an end-to-end hierarchical ensemble framework for taxonomic classification. HiTaxon facilitates data collection and processing, reference database construction and optional training of ML models to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. In addition, through exploring hierarchical methods for HiTaxon, we highlight that our custom approach to hierarchical ensembling improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensembles over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally derived reads. Availability and implementation: HiTaxon is available at: https://github.com/ParkinsonLab/HiTaxon.