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bioRxiv · 10.64898/2026.05.20.726564

ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics

Ghadermazi, P.·Emerson, J. B.·Olm, M. R.
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Abstract

Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500x faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain.

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Ghadermazi, P., Emerson, J. B., Olm, M. R.. 2026-05-22. ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics. https://doi.org/10.64898/2026.05.20.726564

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