zipstrain 0.11.3

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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

Matrix-store workflow dependencies:

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

Cite

If you use ZipStrain in your research, please cite the preprint:

Ghadermazi P, Emerson JB, Olm MR. 2026. ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics. bioRxiv. DOI: 10.64898/2026.05.20.726564

GitHub citation metadata is provided in CITATION.cff:

• https://github.com/OlmLab/ZipStrain/blob/main/CITATION.cff

License

ZipStrain is distributed under the MIT License.