Software: PanPhlAn (Pangenome-based Phylogenomic Analysis)
Description
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.
Available Versions
| Unspecified: | 3.1 |
|---|
For more information, please check its home page: http://segatalab.cibio.unitn.it/tools/panphlan/.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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