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Related Experiment Video

Updated: May 17, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Realfreq: real-time base modification analysis for nanopore sequencing.

Suneth Samarasinghe^1,2,3, Ira Deveson^2,3,4, Hasindu Gamaarachchi^1,2,3

¹School of Computer Science and Engineering, UNSW Sydney, NSW 2052, Kensington, Australia.

Bioinformatics (Oxford, England)

|April 7, 2025

Summary

This summary is machine-generated.

Realfreq provides real-time base modification frequencies during nanopore sequencing. This framework enables live analysis, significantly reducing result turnaround times for researchers using nanopore sequencers.

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Last Updated: May 17, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

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

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

Published on: March 11, 2020

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Nanopore sequencing technology offers real-time data output.
Traditional analysis methods often involve delays between sequencing completion and result availability.
The need for rapid analysis of sequencing data is crucial in many research applications.

Purpose of the Study:

To introduce realfreq, a novel framework for real-time base modification frequency analysis.
To enable live data interpretation during nanopore sequencing runs.
To reduce the overall time from sequencing to actionable results.

Main Methods:

Realfreq is implemented in C programming language and shell scripts.
The framework processes sequencing data in real-time as it is generated.
It calculates and provides access to base modification frequencies during operation.

Main Results:

Realfreq successfully obtains real-time base modification frequencies.
The framework's data analysis rate is sufficient for live analysis on standard hardware.
A laptop can keep pace with a MinION sequencer, and a desktop with a PromethION 2 solo flowcell.

Conclusions:

Realfreq facilitates real-time analysis of nanopore sequencing data.
This capability significantly shortens the time required to obtain sequencing results.
The framework enhances the efficiency of genomic research workflows.