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Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode.

Son Hoang Nguyen1, Tania P S Duarte1, Lachlan J M Coin1

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Bioinformatics (Oxford, England)
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Summary

We developed npBarcode, a new bioinformatics tool for real-time demultiplexing of Oxford Nanopore sequencing reads. This tool enables streaming analysis, overcoming limitations of existing methods for multiplexed sequencing applications.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Oxford Nanopore sequencing now supports barcoding, enhancing its utility.
  • Existing bioinformatics tools for demultiplexing barcoded reads lack streaming analysis capabilities.
  • This limitation hinders real-time applications, a key advantage of Nanopore technology.

Purpose of the Study:

  • To introduce npBarcode, a novel bioinformatics tool for real-time barcode demultiplexing.
  • To enable streaming analysis of multiplexed Oxford Nanopore sequencing data.
  • To facilitate real-time applications by overcoming limitations of current tools.

Main Methods:

  • Developed npBarcode, an open-source, cross-platform tool for streaming barcode demultiplexing.
  • Integrated npBarcode into npReader, providing a graphical user interface (GUI).
  • The tool allows concurrent monitoring of sequencing progress during analysis.

Main Results:

  • npBarcode performs barcode demultiplexing in a streaming fashion.
  • The tool achieves accuracy comparable to or better than existing methods.
  • The integrated GUI allows users to monitor sequencing progress in real-time.

Conclusions:

  • npBarcode enhances the real-time capabilities of multiplexed Oxford Nanopore sequencing.
  • The tool supports piping data for immediate downstream analyses.
  • npBarcode is available as part of the Japsa toolkit for genome analysis.