refgenconf

What it is and what it does

refgenconf is a configuration object library for managing reference genome assemblies in bioinformatics workflows. It provides a standardized way to organize, store, and access metadata and resource paths for genome data—the kind of structured configuration that tools like refgenie depend on. The package wraps common genome assembly information (sequences, annotations, indices) into a consistent Python object model, so downstream tools can reliably locate and reference genome resources without hardcoding paths or formats.

The package is built on standard Python libraries (pyyaml for config parsing, requests for remote access, rich for terminal output, tqdm for progress tracking) and specialized bioinformatics tools (pyfaidx for FASTA indexing, yacman for configuration management). It targets Python 3.10 and later and is actively maintained, with recent releases indicating ongoing development.

Use it for:

• Store and retrieve reference genome metadata and resource paths in a standardized format for bioinformatics pipelines
• Integrate genome configuration into tools that need reliable, structured access to assembly data
• Manage multiple genome assemblies and their associated indices in a single configuration object
• Enable reproducible bioinformatics workflows by centralizing genome resource definitions

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Manages standardized configuration for reference genome assemblies, providing a structured way to organize and access genome metadata and resource paths used by refgenie and related bioinformatics tools.

Yes, if you are building or using bioinformatics tools that work with reference genomes. The package is actively maintained, has low install friction, carries a permissive license, and addresses a real need for standardized genome configuration. Install it if refgenie or a tool depending on refgenconf is part of your workflow.

Install

refgenconf on PyPI

pip install refgenconf

uv add refgenconf

poetry add refgenconf

Installing refgenconf

Before you install

Low friction installation with a pure Python wheel. Active maintenance status and support for current Python versions (3.10–3.14) indicate ongoing support.

License in practice

BSD-2-Clause is a permissive open-source license; you can use, modify, and distribute this package with minimal restrictions, provided you retain the license notice.

Quickstart

pip install refgenconf

from refgenconf import RefGenConf
config = RefGenConf()
# Access or manage genome assembly configuration

Requires Python 3.10 or later; intended for use within bioinformatics workflows that provide or reference genome assembly data.

Verify before relying

• Whether refgenconf can be used standalone or requires refgenie to be installed separately
• What the typical workflow is for end users versus tool developers integrating it

Package facts

Evidence: refgenconf-0.13.1-py3-none-any.whl

Keywords: bioinformatics, sequencing, ngs

Tags

More Bio-Informatics packages