https://github.com/berntpopp/muconeup
MucOneUp simulates diploid MUC1 VNTR references with variable repeats, targeted mutations, and toxic protein detection. It also integrates an Illumina read simulation pipeline for comprehensive genomic benchmarking.
https://github.com/berntpopp/muconeup
bioinformatics genomics muc1 orf python simulation vntr
Last synced: 3 months ago
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MucOneUp simulates diploid MUC1 VNTR references with variable repeats, targeted mutations, and toxic protein detection. It also integrates an Illumina read simulation pipeline for comprehensive genomic benchmarking.
- Host: GitHub
- URL: https://github.com/berntpopp/muconeup
- Owner: berntpopp
- Created: 2025-01-30T20:32:07.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-04-04T22:10:27.000Z (3 months ago)
- Last Synced: 2026-04-05T00:14:48.616Z (3 months ago)
- Topics: bioinformatics, genomics, muc1, orf, python, simulation, vntr
- Language: Python
- Homepage:
- Size: 22 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
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README
# MucOneUp
[](https://www.python.org/downloads/)
[](https://github.com/berntpopp/MucOneUp/actions)
[](https://berntpopp.github.io/MucOneUp/)
[](https://github.com/berntpopp/MucOneUp/pkgs/container/muconeup%2Fmuconeup)
[](https://opensource.org/licenses/MIT)
MUC1 VNTR simulation and analysis toolkit for genomics research.
---
## Overview
MucOneUp generates realistic **MUC1 Variable Number Tandem Repeat (VNTR) sequences** with customizable mutations and platform-specific sequencing reads. Designed for benchmarking variant callers, testing mutation detection pipelines, and generating synthetic training data.
**Key Capabilities:**
- Diploid haplotype generation with probability-based repeat transitions
- Frameshift mutation simulation (dupC, delC, custom insertions/deletions)
- Multi-platform read simulation (Illumina, Oxford Nanopore, PacBio HiFi)
- ORF prediction with toxic protein detection for ADTKD-MUC1 analysis
- SNP integration and VNTR statistics analysis
- Reproducible workflows with seed-based generation
---
## Quick Start
```bash
# View help and version (no --config required)
muconeup -h # Show help
muconeup -V # Show version
# Generate diploid haplotypes with mutation
muconeup --config config.json simulate \
--out-base sample \
--mutation-name dupC \
--mutation-targets 1,25
# Predict ORFs and detect toxic proteins
muconeup --config config.json analyze orfs \
sample.001.simulated.fa \
--out-base orfs
# Simulate Illumina reads
muconeup --config config.json reads illumina \
sample.001.simulated.fa \
--coverage 100
```
**Documentation:** https://berntpopp.github.io/MucOneUp/
---
## Installation
### Option 1: pip (Recommended for Users)
```bash
pip install git+https://github.com/berntpopp/MucOneUp.git
```
**Requirements:**
- Python 3.10+
- External tools for read simulation (optional): BWA, samtools, reseq
### Option 2: Docker (All-in-One)
```bash
# Pull image
docker pull ghcr.io/berntpopp/muconeup/muconeup:latest
# Run
docker run --rm \
-v $(pwd)/data:/data \
-v $(pwd)/config.json:/app/config.json:ro \
ghcr.io/berntpopp/muconeup/muconeup:latest \
--config /app/config.json \
simulate --out-base /data/sample
```
**Includes:** MucOneUp + Illumina (w-Wessim2) + ONT (NanoSim) + PacBio (pbsim3) - pre-configured environment.
### Option 3: Development Setup
```bash
# Clone repository
git clone https://github.com/berntpopp/MucOneUp.git
cd MucOneUp
# Install with uv (modern Python package manager)
make init # Install dev dependencies + pre-commit hooks
make test # Run 568 tests
make check # Verify installation
```
---
## Citation
If you use MucOneUp in your research:
```bibtex
@software{muconeup2025,
author = {Popp, Bernt},
title = {MucOneUp: MUC1 VNTR Simulation and Analysis Toolkit},
year = {2025},
url = {https://github.com/berntpopp/MucOneUp},
note = {Version available at https://github.com/berntpopp/MucOneUp/releases}
}
```
**Status:** Pre-release software under active development. A manuscript is in preparation.
---
## License
MIT License - see [LICENSE](LICENSE) for details.
---
**Maintained by:** [Bernt Popp](https://github.com/berntpopp)