refgenconf
A standardized configuration object for reference genome assemblies
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.10 or later; intended for use within bioinformatics workflows that provide or reference genome assembly data.
- 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 · maintenance · safety
BSD-2-Clause (permissive) — 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.
last release 2026-04-01 (135 days)
0 known vulnerabilities (OSV.dev, 2026-08-14) · 205,016 downloads/mo, #9,593 on PyPI
Alternatives
Verify before relying
pip install refgenconf
from refgenconf import RefGenConf
config = RefGenConf()
# Access or manage genome assembly configuration- 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
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 on it.
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
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.
Requires Python 3.10 or later; intended for use within bioinformatics workflows that provide or reference genome assembly data.
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 configurationVerify 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
| License | BSD-2-Clause permissive |
| Python support | Supports the current Python release >=3.10 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 7 packagespyfaidxpyyamlrequestsrichubiquergyacmantqdm |
| Maintenance | Actively maintained 135 days since the last release |
| First released | |
| Downloads | 205,016 / month, #9,593 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: refgenconf-0.13.1-py3-none-any.whl
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See also refgenie · edam-ontology · cg · biocommons.seqrepo · peppy · eido · fair-esm · pyensembl · bx-python · multiqc