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Strain-resolution metagenomics at scale. ZipStrain is a Python package specializing in strain-level metagenomic analysis. It profiles mapped reads into per-position nucleotide counts and compares metagenomic samples at genome and gene scope. ZipStrain is designed for large datasets, with an accompanying nextflow pipeline (See the documentation - https://olmlab.github.io/ZipStrain)
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Developed by Parsa Ghadermazi and the Olm Lab, University of Colorado Boulder.
Strain-level metagenomics in three commands: ZipStrain maps reads, profiles them at single-nucleotide resolution, and compares samples by ANI to tell whether they share a strain.
Full documentation available at https://olmlab.github.io/ZipStrain/
# Conda (recommended — bundles samtools and the map aligners)
conda create -n zipstrain -c conda-forge -c bioconda python=3.12 zipstrain bowtie2 samtools sylph
conda activate zipstrain
zipstrain testPrefer pip? pip install zipstrain (then install samtools separately). Full options: Installation.
Aligns reads to a reference and writes sorted BAMs plus a samples.txt ready for profiling. Omit --reference-fasta to let Sylph pick and build a reference automatically. Resumable if interrupted.
zipstrain map -i reads.csv -o mapped \
--reference-fasta ref.fna --stb-file ref.stb
Counts A/C/G/T at every reference position and writes per-genome stats (coverage, breadth, a present/absent call) and SNVs. Missing assets are auto-generated and cached.
zipstrain profile -i mapped/samples.txt -f ref.fna -s ref.stb -r profiled
Compares every pair of samples by popANI (near 100% ⇒ same strain). Point --profile-db at a CSV of profile_name,profile_location.
zipstrain compare --profile-db profiles.csv -r compared
Every run writes a zipstrain_run.log so you can tell if it is running, finished, or crashed. Prefer a pipeline? A Nextflow implementation runs all of this end to end.
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. https://doi.org/10.64898/2026.05.20.726564
GitHub can also expose the citation metadata directly from CITATION.cff.
ZipStrain is distributed under the terms described in LICENSE.