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 1.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| zipstrain-1.2.0.tar.gz | 170.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| zipstrain-1.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 349.4 kB
Release files / zipstrain-1.2.0.tar.gz
| Download URL | zipstrain-1.2.0.tar.gz |
|---|---|
| Size | 170.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
8d80b751972b06c875c873e24e0ad60963f78f72dd1601cca0d581d88c16a4ad
|
|
BLAKE2b-256 checksum How to use checksums |
25cc0d88100d13bea96c6c4ee7099f9c3c13f706f97a3168c7e514dde2871bae
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 25, 2026.
Transparency logRelease files / zipstrain-1.2.0-py3-none-any.whl
| Download URL | zipstrain-1.2.0-py3-none-any.whl |
|---|---|
| Size | 179.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
359ac13ce6df8f54960df8347c32ea5da453d64abad834f0cdec871376af2233
|
|
BLAKE2b-256 checksum How to use checksums |
15873b36cd489eb8fe6cac3c4eec13c6712abed17b49bf4cf002b22d170721fd
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 25, 2026.
Transparency log
