Strain-level metagenomic profiling using pangenome graphs with PanTax.

ABSTRACT: Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, most existing strain-level taxonomic classifiers rely on the sequence representation of multipl

SUBMITTER: Zhang W 

PROVIDER: S-EPMC12863173 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature