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