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Updated: May 17, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
Realfreq: real-time base modification analysis for nanopore sequencing
Suneth Samarasinghe1,2,3, Ira Deveson2,3,4, Hasindu Gamaarachchi1,2,3
1School of Computer Science and Engineering, UNSW Sydney, NSW 2052, Kensington, Australia.
Summary:
Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is running, reducing the turnaround time of the results. We introduce realfreq, a framework for obtaining real-time base modification frequencies while a nanopore sequencer is in operation. Realfreq calculates and allows access to the real-time base modification frequency results while the sequencer is running. We demonstrate that the data analysis rate with realfreq on a laptop computer can keep up with the output data rate of a nanopore MinION sequencer, while a desktop computer can keep up with a single PromethION 2 solo flowcell.
Availability And Implementation:
Realfreq is a free and open-source application implemented in C programming language and shell scripts. The source code and the documentation for realfreq can be found at https://github.com/imsuneth/realfreq. The version used for the manuscript is also available at https://doi.org/10.5281/zenodo.15128668.
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