For any help see :
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 speciespanphlan_map.py
, to profile each metagenomic sample by mapping it against the species of interestpanphlan_profile.py
, to merge and process the mapping results in order to get the final gene presence/absence matrixFor 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:
And the following Python libraries:
PanPhlAn is also available in bioconda :
conda install -c bioconda panphlan
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