MucOneUp

MUC1 VNTR simulation and analysis toolkit for genomics research.

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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

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Quick Start

# 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/

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Installation

Option 1: pip (Recommended for Users)

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)

# 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

# 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

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Citation

If you use MucOneUp in your research:

@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.

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License

MIT License - see LICENSE for details.

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Maintained by: Bernt Popp