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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
torchwheel 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
samtoolsto be installed separately when using pip.
Verify
zipstrain --version
zipstrain test
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