Welcome to ZipStrain

ZipStrain is a toolkit for strain-level metagenomic profiling and comparison. It supports both the standard profile-table comparison workflow and the matrix-store workflow for repeated large all-vs-all comparisons.

What ZipStrain Does

ZipStrain helps you:

• profile mapped metagenomic samples at nucleotide resolution
• compare samples at the genome level with ANI and IBS
• compare samples at the gene level
• scale to larger cohorts with resumable matrix-store comparisons
• run either from the CLI, the Python API, or the bundled Nextflow pipeline

Comparison Routes

ZipStrain now supports two comparison styles:

1. Standard profile compare
2. compares profile parquets directly through table operations

3. best when one run needs to evaluate many genomes at the same time

4. Matrix compare

5. builds a reusable matrix store from profile parquets
6. best for repeated many-sample comparisons focused on one genome or a small set of genomes
7. supports resumable compare databases and optional gene ANI

If you are new to the project, start with the Tutorial. It now includes worked examples for:

• the standard Python/CLI workflow
• the standard Nextflow workflow
• the matrix-store workflow

Documentation Map

• Tutorial: end-to-end workflow plus worked examples for standard CLI, standard Nextflow, and matrix compare
• CLI Reference: command-by-command usage
• Installation: environment setup and optional matrix dependencies
• Nextflow Pipeline: pipeline execution details
• API Reference: Python modules and programmatic entry points

Highlights

• Strain-level resolution: profile and compare samples at nucleotide resolution
• Multiple execution routes: standard profile compare, matrix compare, and Nextflow workflows
• Resumability: matrix compare writes resumable DuckDB result databases
• Scalability: supports CPU, CUDA, and Apple Silicon torch backends for matrix compare
• Container support: Docker and Apptainer/Singularity friendly