poppunk
Link to section 'Introduction' of '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.
Docker hub: https://hub.docker.com/r/staphb/poppunk
Home page: https://github.com/bacpop/PopPUNK
Link to section 'Versions' of 'poppunk' Versions
- 2.5.0
- 2.6.0
Link to section 'Commands' of 'poppunk' 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
Link to section 'Module' of 'poppunk' Module
You can load the modules by:
module load biocontainers
module load poppunk
Link to section 'Example job' of 'poppunk' 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 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