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BioDemuX.jl

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Overview

BioDemuX.jl is a Julia package designed for demultiplexing reads based on barcodes. Given a set of sequencing reads in FASTQ format and a reference barcode in CSV or TSV format, each read is assigned to a FASTQ file corresponding to its barcode. This barcode assignment process is designed to be robust to barcode mutations and allows you to adjust the permitted level of mutation through parameters.

conceptual_diagram

Key Features

  • Ultara-Fast Semi-Global Alignment: Unrivaled speed with robust handling of indels and mismatches.
  • Extensive Flexibility: Custom search ranges, dual barcoding, adapter trimming, and multi-mode matching (:semiglobal, :hamming, :exact).
  • High-Performance Architecture: Multi-threaded streaming for efficient memory usage.
  • Visualize Analysis: Optional interactive HTML reports.
  • Zero-Dependency CLI: Standalone binary for easy deployment.

References

To be published.

Installation

  1. Open the Julia REPL (by typing julia in the terminal).
  2. Press ] to enter the Pkg REPL mode.
  3. Run the following command to install BioDemuX.jl: julia add BioDemuX
  4. Press the Backspace key to exit the Pkg mode.

Dataset

The datasets used in the paper are publicly available.

  • In vitro dataset and test code:

Link to the dataset and test code: https://doi.org/10.24433/CO.5417078.v1

  • In silico dataset:

Link to the dataset: https://doi.org/10.5281/zenodo.14178228

Support or Contact

If you encounter any issues or have requests, please provide feedback by posting a new GitHub issue on our repository. We appreciate your input and will do our best to assist you!