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OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.

Simone Marini1,2, Alexander Barquero3, Anisha Ashok Wadhwani3

  • 1Department of Epidemiology, University of Florida, Gainesville, USA.

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|April 1, 2024
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Summary
This summary is machine-generated.

Portable genomic sequencing analysis is now possible on smartphones with OCTOPUS software. This tool enhances metagenomic classification accuracy for Nanopore data, reducing false positives in field applications.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Portable genomic sequencers like Oxford Nanopore's MinION offer real-time applications in clinical and environmental health.
  • Downstream bioinformatics analysis of genomic data faces bottlenecks, especially when cloud processing is unavailable or only low-end devices are accessible.

Purpose of the Study:

  • To develop a platform-friendly software for portable metagenomic analysis of Nanopore sequencing data.
  • To address the limitations of existing bioinformatics pipelines in resource-constrained or offline environments.

Main Methods:

  • Developed OCTOPUS (Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons), a Java-based software.
  • Reimplemented features from Kraken2 and KrakenUniq, incorporating novel components for improved classification on incomplete reference databases.
  • Optimized the software for execution on mobile devices such as smartphones and tablets.

Main Results:

  • OCTOPUS achieves sensitivity and precision comparable to Kraken2 for metagenomic classification.
  • Demonstrated a significant reduction in the false positive rate, ranging from 4- to 16-fold compared to existing tools.
  • Validated performance on real-world data, showing a high correlation with expected results.

Conclusions:

  • OCTOPUS provides an efficient and accurate solution for portable metagenomic analysis of Nanopore data.
  • The software is suitable for deployment on mobile devices, overcoming limitations of connectivity and computing power.
  • OCTOPUS enhances the utility of portable sequencing in field-based clinical and environmental health applications.