panphlan
Link to section 'Introduction' of '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/.
Link to section 'Versions' of 'panphlan' Versions
- 3.1
Link to section 'Commands' of 'panphlan' Commands
- panphlan_download_pangenome.py
- panphlan_map.py
- panphlan_profiling.py
Link to section 'Module' of 'panphlan' Module
You can load the modules by:
module load biocontainers
module load panphlan
Link to section 'Example job' of 'panphlan' Example job
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