zipstrain 0.8.5

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ZipStrain

ZipStrain is a strain-resolution metagenomics toolkit for profiling mapped reads into nucleotide-count tables and comparing samples at genome and gene resolution.

Documentation:

• Docs: https://OlmLab.github.io/ZipStrain/
• Repository: https://github.com/OlmLab/ZipStrain

Install

Base install:

pip install zipstrain

Experimental matrix utilities with Torch-backed execution:

pip install "zipstrain[matrix]"

Notes:

• Apple Silicon can use the standard torch wheel with the MPS backend.

• Linux CUDA installs should replace Torch with the matching CUDA wheel from PyTorch:

  pip install "zipstrain[matrix]"
  pip install --upgrade torch --index-url https://download.pytorch.org/whl/cu124
  

• Profiling requires samtools to be installed separately when using pip.

Verify

zipstrain --version
zipstrain test