poppunk 2.6.1-foss-2022a

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.

Accessing poppunk 2.6.1-foss-2022a

To load the module for poppunk 2.6.1-foss-2022a please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2022a
module load poppunk/2.6.1-foss-2022a

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Extensions

• poppunk 2.6.1
• treeswift 1.1.33

More Information

For more information visit the poppunk website.

Dependencies

This version of poppunk has a direct dependency on: Biopython/1.79-foss-2022a Boost/1.79.0-GCC-11.3.0 Eigen/3.4.0-GCCcore-11.3.0 foss/2022a graph-tool/2.55-foss-2022a h5py/3.7.0-foss-2022a HDBSCAN/0.8.29-foss-2022a mandrake/1.2.2-foss-2022a matplotlib/3.5.2-foss-2022a networkx/2.8.4-foss-2022a numba/0.56.4-foss-2022a pp-sketchlib/2.1.1-foss-2022a pybind11/2.9.2-GCCcore-11.3.0 Python/3.10.4-GCCcore-11.3.0 rapidNJ/2.3.3-GCCcore-11.3.0 scikit-learn/1.1.2-foss-2022a SciPy-bundle/2022.05-foss-2022a tqdm/4.64.0-GCCcore-11.3.0 X11/20220504-GCCcore-11.3.0

Last modified on 15th November 2023