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
panphlan_map.py, to profile each metagenomic sample by mapping it against the species specific database
panphlan_profile.py, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices
PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:
- Python 3.x (including the Biopython module)
For more information, see our wiki Download and Installation.