PanPhlAn

Introduction

PanPhlAn (Pangenome-based Phylogenomic Analysis) is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.

For more information, please check its home page: http://segatalab.cibio.unitn.it/tools/panphlan/.

Versions

  • 3.1

Commands

  • panphlan_download_pangenome.py

  • panphlan_map.py

  • panphlan_profiling.py

Module

You can load the modules by:

module load biocontainers
module load panphlan

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run PanPhlAn on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=panphlan
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers panphlan