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It is designed to be the definitive tool for accurate and efficient barcode assignment.\n\n## 🚀 Key Features\n\n*   **⚡ Ultra-Fast Semi-Global Alignment**:\n    *   The core engine is built on highly optimized semi-global alignment. It delivers **unrivaled speed** while robustly handling **insertions, deletions (indels)**, and mismatches—recovering reads that standard Hamming-based tools discard.\n\n*   **🔧 Extensive Flexibility**:\n    *   **Precise Targeting**: Define custom search ranges to focus on specific regions.\n    *   Supports **Dual Barcoding** and variable-length barcodes.\n    *   **Adapter Trimming**: Support for simultaneous adapter matching and trimming.\n    *   **Multi-Mode Matching**: Choose between `:semiglobal` for robustness, or `:hamming`/`:exact` for speed.\n\n*   **🚀 High-Performance Architecture**:\n    *   Multi-threaded \u0026 Channel-based streaming.\n    *   Efficient memory usage via streaming I/O.\n\n*   **📊 Visualize Analysis**:\n    *   Optional interactive **HTML reports** for distribution and score analysis.\n\n*   **💻 Zero-Dependency CLI**:\n    *   Available as a standalone binary for Linux, macOS, and Windows. No Julia installation required to run in production pipelines.\n\n## 📚 Documentation\n\n**[Full Documentation](https://I-Mihara.github.io/BioDemuX.jl/)**\n\nVisit our documentation for comprehensive guides, API references, and detailed usage examples.\n\n## 📦 Installation\n```julia\nusing Pkg; Pkg.add(\"BioDemuX\")\n```\n\n## 🏃 Quick Start\n\n```julia\nusing BioDemuX\nexecute_demultiplexing(\"reads.fastq\", \"barcodes.csv\", \"output_dir\")\n```\n\n**[CLI Users]** Download the binary from [Releases](https://github.com/I-Mihara/BioDemuX.jl/releases) and run:\n```bash\n./biodemux reads.fastq barcodes.csv output_dir\n```\n\n## 👥 Support\nIf you encounter any issues, please open an issue on [GitHub](https://github.com/I-Mihara/BioDemuX.jl/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fi-mihara%2Fbiodemux.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fi-mihara%2Fbiodemux.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fi-mihara%2Fbiodemux.jl/lists"}