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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 infectious outbreak epidemiology and microbial population studies.

• Download the PanPhlAn software
• The PanPhlAn steps
• Applications and examples
• Version history

For a detailed tutorial with a small example dataset, see Tutorial. For help, use the bioBakery help forum.

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

If you use PanPhlAn 3, 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, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata. bioRxiv preprint (2020)

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Download the PanPhlAn software

PanPhlAn can be manually installed by downloading the GitHub repository

git clone https://github.com/SegataLab/panphlan.git

or retrieved using pip

pip install panphlan

or BioConda

conda install -c bioconda panphlan

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

• Python 3 (version 3.8+ is recommended) including packages :
  • numpy
  • scipy
  • pandas
• bowtie2 (version 2.4 is recommended)
• samtools (version 1.11 is recommended)

The PanPhlAn steps

1. Download pangenome
   Download the files needed for mapping

   panphlan_download_pangenome.py -i Eubacterium_rectale`
   

2. PanPhlAn mapping

   Map each metagenomic sample against the species database. Example: screen for E. rectale pangenome genes in sample01 and sample02

   panphlan_map.py -p Eubacterium_rectale/Eubacterium_rectale_pangenome.tsv \
                   --indexes Eubacterium_rectale/Eubacterium_rectale \    
                   -i sample01.fastq \
                   -o map_results/sample01_erectale.csv
   
   panphlan_map.py -p Eubacterium_rectale/Eubacterium_rectale_pangenome.tsv \
                   --indexes Eubacterium_rectale/Eubacterium_rectale \    
                   -i sample02.fastq \
                   -o map_results/sample02_erectale.csv                   
   

3. PanPhlAn profiling
   Merge and process the mapping results to generate the final gene-family presence/absence profile matrix

   panphlan_profiling.py -i map_results/ \
                         --o_matrix result_profile_erectale.tsv \ 
                         -p Eubacterium_rectale/Eubacterium_rectale_pangenome.tsv \
                         --add_ref