panaroo
Link to section 'Introduction' of 'panaroo' Introduction
Panaroo is an updated pipeline for pangenome investigation.
BioContainers: https://biocontainers.pro/tools/panaroo
Home page: https://github.com/gtonkinhill/panaroo
Link to section 'Versions' of 'panaroo' Versions
- 1.2.10
Link to section 'Commands' of 'panaroo' Commands
- panaroo
- panaroo-extract-gene
- panaroo-filter-pa
- panaroo-fmg
- panaroo-gene-neighbourhood
- panaroo-img
- panaroo-integrate
- panaroo-merge
- panaroo-msa
- panaroo-plot-abundance
- panaroo-qc
- panaroo-spydrpick
Link to section 'Module' of 'panaroo' Module
You can load the modules by:
module load biocontainers
module load panaroo
Link to section 'Example job' of 'panaroo' 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 panaroo on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=panaroo
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers panaroo
panaroo -i gff/*.gff -o results --clean-mode strict