ZipStrain
Fast strain-level metagenomics in three commands: map reads to BAMs,
profile them into per-position nucleotide-count tables, and compare
samples by ANI to tell whether they share a strain.
Documentation:
- Docs: https://OlmLab.github.io/ZipStrain/
- Repository: https://github.com/OlmLab/ZipStrain
Install
Conda is the easiest path — it brings in samtools and the map aligners too:
conda create -n zipstrain -c conda-forge -c bioconda \
python=3.12 zipstrain bowtie2 samtools sylph
Or with pip (into a fresh virtual environment):
pip install zipstrain
Matrix-store comparison dependencies (compare --method matrix):
pip install "zipstrain[matrix]"
Notes:
-
With pip, install
samtoolsseparately (profiling needs it);zipstrain mapadditionally needsbowtie2andsylph(andprodigalfor--predict-genes). -
On Apple Silicon, use a native
osx-arm64Conda so dependencies install natively; the standardtorchwheel uses 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
See the installation guide for full details.
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:
License
ZipStrain is distributed under the MIT License.
1 maintainer
Release files for zipstrain 1.1.0
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Source distribution (sdist)
| File | Size | Uploaded | |
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| zipstrain-1.1.0.tar.gz | 168.7 kB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| zipstrain-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 345.9 kB
Release files / zipstrain-1.1.0.tar.gz
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