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Designed for benchmarking variant callers, testing mutation detection pipelines, and generating synthetic training data.\n\n**Key Capabilities:**\n\n- Diploid haplotype generation with probability-based repeat transitions\n- Frameshift mutation simulation (dupC, delC, custom insertions/deletions)\n- Multi-platform read simulation (Illumina, Oxford Nanopore, PacBio HiFi)\n- ORF prediction with toxic protein detection for ADTKD-MUC1 analysis\n- SNP integration and VNTR statistics analysis\n- Reproducible workflows with seed-based generation\n\n---\n\n## Quick Start\n\n```bash\n# View help and version (no --config required)\nmuconeup -h        # Show help\nmuconeup -V        # Show version\n\n# Generate diploid haplotypes with mutation\nmuconeup --config config.json simulate \\\n  --out-base sample \\\n  --mutation-name dupC \\\n  --mutation-targets 1,25\n\n# Predict ORFs and detect toxic proteins\nmuconeup --config config.json analyze orfs \\\n  sample.001.simulated.fa \\\n  --out-base orfs\n\n# Simulate Illumina reads\nmuconeup --config config.json reads illumina \\\n  sample.001.simulated.fa \\\n  --coverage 100\n```\n\n**Documentation:** https://berntpopp.github.io/MucOneUp/\n\n---\n\n## Installation\n\n### Option 1: pip (Recommended for Users)\n\n```bash\npip install git+https://github.com/berntpopp/MucOneUp.git\n```\n\n**Requirements:**\n- Python 3.10+\n- External tools for read simulation (optional): BWA, samtools, reseq\n\n### Option 2: Docker (All-in-One)\n\n```bash\n# Pull image\ndocker pull ghcr.io/berntpopp/muconeup/muconeup:latest\n\n# Run\ndocker run --rm \\\n  -v $(pwd)/data:/data \\\n  -v $(pwd)/config.json:/app/config.json:ro \\\n  ghcr.io/berntpopp/muconeup/muconeup:latest \\\n  --config /app/config.json \\\n  simulate --out-base /data/sample\n```\n\n**Includes:** MucOneUp + Illumina (w-Wessim2) + ONT (NanoSim) + PacBio (pbsim3) - pre-configured environment.\n\n### Option 3: Development Setup\n\n```bash\n# Clone repository\ngit clone https://github.com/berntpopp/MucOneUp.git\ncd MucOneUp\n\n# Install with uv (modern Python package manager)\nmake init    # Install dev dependencies + pre-commit hooks\nmake test    # Run 568 tests\nmake check   # Verify installation\n```\n\n---\n\n## Citation\n\nIf you use MucOneUp in your research:\n\n```bibtex\n@software{muconeup2025,\n  author = {Popp, Bernt},\n  title = {MucOneUp: MUC1 VNTR Simulation and Analysis Toolkit},\n  year = {2025},\n  url = {https://github.com/berntpopp/MucOneUp},\n  note = {Version available at https://github.com/berntpopp/MucOneUp/releases}\n}\n```\n\n**Status:** Pre-release software under active development. A manuscript is in preparation.\n\n---\n\n## License\n\nMIT License - see [LICENSE](LICENSE) for details.\n\n---\n\n**Maintained by:** [Bernt Popp](https://github.com/berntpopp)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fberntpopp%2Fmuconeup","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fberntpopp%2Fmuconeup","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fberntpopp%2Fmuconeup/lists"}