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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.

Richard M Leggett¹, Darren Heavens¹, Mario Caccamo¹

¹The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK.

Bioinformatics (Oxford, England)

|September 19, 2015

Summary

NanoOK is a new open-source software for comprehensive quality control of Oxford Nanopore MinION sequencing data. It provides detailed analysis of error profiles, quality, and yield for metagenomic and multiplexed samples.

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Last Updated: Apr 3, 2026

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The Oxford Nanopore MinION offers real-time, long-read sequencing from a portable device.
Existing tools lack comprehensive alignment-based quality control for rapidly evolving Nanopore technology.
Essential quality control is needed for MinION Access Programme (MAP) data.

Purpose of the Study:

To develop NanoOK, an open-source software for in-depth quality control and error profile analysis of Nanopore sequencing data.
To provide detailed yield, quality, and error metrics for MinION data.
To support multi-reference analysis for metagenomic and multiplexed samples.

Main Methods:

NanoOK is implemented in Java with supporting R scripts.
The software supports multiple Nanopore aligners and is extensible.
Tested on Linux and Mac OS X.

Main Results:

NanoOK generates comprehensive tabular, graphical, and multi-page PDF reports.
Detailed error profiles, quality, and yield data are provided.
Supports multi-reference analysis for complex samples.

Conclusions:

NanoOK addresses the need for advanced quality control in Nanopore sequencing.
The software facilitates robust analysis of MinION data, including metagenomics.
Open-source availability and multiple platform support enhance its utility.