For any help see :

• The PanPhlan wiki
• The PanPhlAn step-by-step tutorial
• The bioBakery help forum for overall discussions on various metagenomics softwares. (Purely technical issues should better be raised on GitHub than on the forum.)

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition 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 microbial population studies.

PanPhlAn is written in Python and covers the 3 main tasks:

• panphlan_download_pangenome.py, to download pangenome files (fasta file of contigs, BowTie2 indexes and general information) for over 3,000 species
• panphlan_map.py, to profile each metagenomic sample by mapping it against the species of interest
• panphlan_profile.py, to merge and process the mapping results in order to get the final gene presence/absence matrix

For custom pangenome generation (advanced) see the PanPhlAn exporter

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

• Bowtie2 (bowtie2 >=2.3.0)
• Samtools (samtools >=1.9)
• Python 3 (python >=3.7)

And the following Python libraries:

• numpy
• pandas
• scipy

PanPhlAn is also available in bioconda :

If you use PanPhlAn, please cite:

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini, Lauren J McIver, Aitor Blanco-Miguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Andrew Maltez Thomas, Paolo Manghi, Matthias Scholz, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata. eLife (2021)

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