README

PanPhlAn 3 - strain detection and characterization

Pangenome-based Phylogenomic Analysis

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 4 main tasks:

• panphlan_download_pangenome.py, to download pangenome files (fasta, 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
• panphlan_find_gene_grp.py, organise OPTICS clustering to find some group of gene with similar profile and assess if they could be mobile elements in the genome. Also plot the presence/absence matrix as Heatmap.

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

• Bowtie2
• Samtools
• Python 3

And the following Python libraries:

• numpy
• pandas
• scipy
• sklearn (only if using panphlan_find_gene_grp.py)
  If visualizations are made, one also needs :
• matplotlib
• seaborn

For any help see the wiki or the bioBakery forum

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