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Related Experiment Video

Updated: May 16, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.

Abdallah Meknas¹, Kyrylo Bessonov¹, Shannon H C Eagle¹

¹National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada.

Access Microbiology

|May 15, 2026

Summary

Sequenoscope is a new bioinformatics pipeline for analyzing Oxford Nanopore Technologies adaptive sampling sequencing data. It successfully demonstrated targeted depletion of Listeria monocytogenes in microbial communities.

Keywords:

Oxford Nanopore Technologies (ONT)adaptive sampling metagenomics method comparison nanopore pipeline sequencing

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Last Updated: May 16, 2026

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Area of Science:

Bioinformatics
Genomics
Microbial Ecology

Background:

Analyzing complex microbial communities requires specialized bioinformatics tools.
Oxford Nanopore Technologies (ONT) adaptive sampling offers targeted sequencing capabilities.
Efficient analysis of adaptive sampling data is crucial for microbial studies.

Purpose of the Study:

To present Sequenoscope, a novel bioinformatics pipeline for ONT adaptive sampling data.
To demonstrate Sequenoscope's utility in analyzing microbial community DNA standards.
To showcase Sequenoscope's ability to compare datasets and assess targeted sequencing efficacy.

Main Methods:

Development of Sequenoscope with three modules: filter_ONT, analyze, and plot.
Application of Sequenoscope to analyze ONT adaptive sampling data from ZymoBIOMICS Microbial Community DNA Standards.
Targeted depletion experiments of Listeria monocytogenes were performed and analyzed.

Main Results:

Sequenoscope successfully filtered reads and generated statistics for adaptive sampling data.
The pipeline confirmed successful depletion of Listeria monocytogenes by analyzing taxon coverage and read data.
Sequenoscope provides interactive visualization for comparing datasets and assessing sequencing parameters.

Conclusions:

Sequenoscope is an effective tool for analyzing ONT adaptive sampling data.
The pipeline facilitates the assessment of targeted sequencing experiments, such as microbial depletion.
Sequenoscope supports cross-platform comparisons, including Illumina short-read data, enhancing its versatility.