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Welcome to ZipStrain

ZipStrain is a tool designed for efficient and scalable strain-level analysis of metagenomic data. It can profile and compare metagenomics samples at nucleotide resolution, providing insights into the strain composition of microbial communities.

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Features

  • Strain-Level Resolution Profiling and Comparison: ZipStrain provides detailed insights into the strain composition of microbial communities, enabling researchers to identify and compare strains across different samples.

  • Scalability: ZipStrain is built using high-performance libraries. This makes comparing samples fast. It also distributes tasks across multiple processors or nodes, making it suitable for large datasets. Finally, most the workflows are resumable.

  • Containerization: ZipStrain is fully containerized using Docker and Singularity, ensuring consistent environments across different platforms and simplifying deployment.

  • Workflow Management: ZipStrain utilizes Nextflow for workflow management, allowing for easy customization, reproducibility, and scalability of analyses.

  • Command-Line Interface (CLI): ZipStrain offers a user-friendly CLI for easy interaction and execution of tasks.

  • Python API: ZipStrain provides a Python API for programmatic access, enabling integration into larger bioinformatics pipelines and workflows. The API also allows for downstream analyses and visualizations.