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PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
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README.md
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README.md

PanPhlAn - strain detection and characterization

Pangenome-based Phylogenomic Analysis

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.

PanPhlAn is written in Python and covers the three main tasks:

  • panphlan_pangenome_generation.py, to create the pangenome database of a bacterial species
    read more
  • panphlan_map.py, to profile each metagenomic sample by mapping it against the species specific database
    read more
  • panphlan_profile.py, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices
    read more

PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:

  • Bowtie2
  • Samtools
  • Python 3.x (including the Biopython module)

For more information, see our wiki Download and Installation.

Contact & User support

A user tutorial is available on the PanPhlAn wiki. For help, use also the bioBakery help forum.

The PanPhlAn software team: Matthias Scholz (algorithm design), Thomas Tolio (programmer), Leonard Dubois and Nicola Segata (principal investigator).


PanPhlAn is a project of the Computational Metagenomics Lab at CIBIO, University of Trento, Italy

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