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Updated: Mar 23, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Matthias Scholz1, Doyle V Ward2, Edoardo Pasolli1
1Centre for Integrative Biology, University of Trento, Trento, Italy.
Abstract:
Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.
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