Poppunk

Introduction

PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/poppunk
Home page: https://github.com/bacpop/PopPUNK

Versions

  • 2.5.0

  • 2.6.0

Commands

  • poppunk

  • poppunk_add_weights.py

  • poppunk_assign

  • poppunk_batch_mst.py

  • poppunk_calculate_rand_indices.py

  • poppunk_calculate_silhouette.py

  • poppunk_easy_run.py

  • poppunk_extract_components.py

  • poppunk_extract_distances.py

  • poppunk_info

  • poppunk_iterate.py

  • poppunk_mandrake

  • poppunk_mst

  • poppunk_references

  • poppunk_visualise

Module

You can load the modules by:

module load biocontainers
module load poppunk

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 poppunk on our clusters:

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

module --force purge
ml biocontainers poppunk