https://github.com/i-mihara/biodemux.jl

High-performance Julia tool for sequence demultiplexing
https://github.com/i-mihara/biodemux.jl

adapter-trimming barcodes bioinformatics-pipeline bioinformatics-software demultiplex demultiplexer demultiplexing demux dms-map-seq dual-barcodes fastq illumina-sequencing julia julia-packages ngs-pipeline sequencing

Last synced: 4 months ago
JSON representation

High-performance Julia tool for sequence demultiplexing

• Host: GitHub
• URL: https://github.com/i-mihara/biodemux.jl
• Owner: I-Mihara
• License: mit
• Created: 2024-09-20T10:36:55.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-12-18T13:28:31.000Z (6 months ago)
• Last Synced: 2025-12-21T16:49:18.620Z (6 months ago)
• Topics: adapter-trimming, barcodes, bioinformatics-pipeline, bioinformatics-software, demultiplex, demultiplexer, demultiplexing, demux, dms-map-seq, dual-barcodes, fastq, illumina-sequencing, julia, julia-packages, ngs-pipeline, sequencing
• Language: Julia
• Homepage:
• Size: 1.09 MB
• Stars: 7
• Watchers: 1
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
![package_logo](BioDemuX_logo.png)

[![Build Status](https://github.com/I-Mihara/BioDemuX.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/I-Mihara/BioDemuX.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Build and Release](https://github.com/I-Mihara/BioDemuX.jl/actions/workflows/release.yml/badge.svg)](https://github.com/I-Mihara/BioDemuX.jl/actions/workflows/release.yml)

[![Docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://I-Mihara.github.io/BioDemuX.jl/)

[![DOI](https://img.shields.io/badge/DOI-10.24433%2FCO.5417078.v2-blue)](https://doi.org/10.24433/CO.5417078.v2)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14191427.svg)](https://doi.org/10.5281/zenodo.14191427)

# BioDemuX.jl

**BioDemuX.jl** is a high-performance Julia package for demultiplexing sequencing reads with robust barcode mutation handling. It is designed to be the definitive tool for accurate and efficient barcode assignment.

## 🚀 Key Features

*   **⚡ Ultra-Fast Semi-Global Alignment**:

    *   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.

*   **🔧 Extensive Flexibility**:

    *   **Precise Targeting**: Define custom search ranges to focus on specific regions.

    *   Supports **Dual Barcoding** and variable-length barcodes.

    *   **Adapter Trimming**: Support for simultaneous adapter matching and trimming.

    *   **Multi-Mode Matching**: Choose between `:semiglobal` for robustness, or `:hamming`/`:exact` for speed.

*   **🚀 High-Performance Architecture**:

    *   Multi-threaded & Channel-based streaming.

    *   Efficient memory usage via streaming I/O.

*   **📊 Visualize Analysis**:

    *   Optional interactive **HTML reports** for distribution and score analysis.

*   **💻 Zero-Dependency CLI**:

    *   Available as a standalone binary for Linux, macOS, and Windows. No Julia installation required to run in production pipelines.

## 📚 Documentation

**[Full Documentation](https://I-Mihara.github.io/BioDemuX.jl/)**

Visit our documentation for comprehensive guides, API references, and detailed usage examples.

## 📦 Installation

```julia

using Pkg; Pkg.add("BioDemuX")

```

## 🏃 Quick Start

```julia

using BioDemuX

execute_demultiplexing("reads.fastq", "barcodes.csv", "output_dir")

```

**[CLI Users]** Download the binary from [Releases](https://github.com/I-Mihara/BioDemuX.jl/releases) and run:

```bash

./biodemux reads.fastq barcodes.csv output_dir

```

## 👥 Support

If you encounter any issues, please open an issue on [GitHub](https://github.com/I-Mihara/BioDemuX.jl/issues).