---
id: refgenie
version: "0.13.0"
license: BSD-2-Clause
license_treatment: permissive
maintenance: active
---

# refgenie — Refgenie creates a standardized folder structure for reference genome files and indexes

License: permissive · Maintenance: active · Downloads: 97.2K/mo

## What it is and what it does

Refgenie is a reference genome resource manager for bioinformatics workflows. It creates and maintains a standardized folder structure for genome files and their associated indexes, making it easier to organize, discover, and reuse genomic data across projects. The package handles the logistics of genome resource management—where files live, how they're named, what indexes exist—so researchers don't have to manually track these details.

The tool is actively maintained, supports Python 3.10 through 3.14, and carries no known security vulnerabilities. Installation is straightforward with a pure Python wheel, making it accessible for integration into existing bioinformatics environments.

Use it for:

- Organize and index multiple reference genomes in a consistent structure for a research group
- Automate genome resource discovery and retrieval within NGS analysis pipelines
- Manage version control and metadata for reference genome collections across projects
- Standardize genome file locations and naming conventions to reduce setup errors
- Integrate genome resource management into reproducible bioinformatics workflows

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

Refgenie manages standardized folder structures and indexes for reference genome files, automating organization and retrieval of genomic resources for bioinformatics workflows.

Yes. Refgenie is actively maintained, carries no security vulnerabilities, installs with low friction, and is licensed permissively under BSD-2-Clause. It solves a genuine organizational problem in genomics workflows. Install it if you work with multiple genomes or need to share genome resources across a team or pipeline.

## Install

pip install refgenie
uv add refgenie
poetry add refgenie

## Installing refgenie

Before you install: Low install friction with a pure Python wheel distribution. Active maintenance status with recent release 170 days ago. Supports Python 3.10 through 3.14.

License in practice: BSD-2-Clause permissive license allows commercial and private use with minimal restrictions, requiring only retention of copyright and license notices.

Quickstart:

pip install refgenie

import refgenie
# Initialize or access a reference genome resource

Requires Python 3.10 or later

Verify before relying:

- Whether refgenie requires external genome data sources or can function standalone
- Performance characteristics when managing large genome collections
- Integration requirements with specific sequencing analysis pipelines

## Package facts

- License: BSD-2-Clause (permissive)
- Python support: supports_current
- Install friction: low
- Maintenance: active
- Downloads: 97.2K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

reference genome manager, genome resource organization, bioinformatics reference data, genome index management, standardized genome structure, ngs reference handling, genomic resource repository, bioinformatics, genome-management, ngs

[View on SkillFed](https://skillfed.io/packages/refgenie) · [View on PyPI](https://pypi.org/project/refgenie/)