# HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification

## TL;DR

HYMET is a new metagenomic tool that improves the accuracy and efficiency of classifying microbial sequences from complex samples.

## Contribution

HYMET introduces a hybrid two-stage design combining adaptive screening and alignment for domain-agnostic classification.

## Key findings

- HYMET achieved a mean F1 score of 83.89% across 7 CAMI datasets with stable performance up to 30% mutation rates.
- It demonstrated near-perfect genus-level concordance in the ZymoBIOMICS Gut Microbiome Standard with a Pearson correlation of 0.998.
- HYMET recovered all bacterial members in the ZymoBIOMICS mock community and showed robustness in real-world human gut metagenomes.

## Abstract

Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a 2–stage hybrid design combining adaptive Mash–based screening with Minimap2 alignment and a coverage–weighted Lowest Common Ancestor classifier. Its sample–adaptive thresholds and on–the–fly reference database construction enable efficient, domain–agnostic classification while maintaining accuracy across divergent genomes.

Across 7 CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus–level F1 of 76.75% and species–level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 \documentclass[12pt]{minimal}
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HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment–anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.

Graphical AbstractFor image description, please refer to the figure legend and surrounding text.