refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.10 or later
- Low install friction with a pure Python wheel distribution.
- Active maintenance status with recent release 170 days ago.
License · maintenance · safety
BSD-2-Clause (permissive) — BSD-2-Clause permissive license allows commercial and private use with minimal restrictions, requiring only retention of copyright and license notices.
last release 2026-02-25 (170 days)
0 known vulnerabilities (OSV.dev, 2026-08-14) · 97,243 downloads/mo, #13,161 on PyPI
Alternatives
Verify before relying
pip install refgenie
import refgenie
# Initialize or access a reference genome resource- 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
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 on this page. Verify before relying on it.
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
refgenie on PyPI
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.
Requires Python 3.10 or later
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 resourceVerify 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 the current Python release >=3.10 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 7 packageslogmusepiperpyfaidxrefgenconfrichubiquergyacman |
| Maintenance | Actively maintained 170 days since the last release |
| First released | |
| Downloads | 97,243 / month, #13,161 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaProgramming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: 3.14Topic :: Scientific/Engineering :: Bio-Informatics |
Evidence: refgenie-0.13.0-py3-none-any.whl
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