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

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	2.5.0, 2.6.0
BELL	2.5.0, 2.6.0
GAUTSCHI	2.5.0, 2.6.0
NEGISHI	2.5.0, 2.6.0
SCHOLAR	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:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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
module biocontainers poppunk

# Your poppunk workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers poppunk

# Your poppunk workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers poppunk

# Your poppunk workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers poppunk

# Your poppunk workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers poppunk

# Your poppunk workflow...