Samarasinghe Suneth, Deveson Ira, Gamaarachchi Hasindu
School of Computer Science and Engineering, UNSW Sydney, NSW 2052, Kensington, Australia.
Genomics and Inherited Disease Program, Garvan Institute of Medical Research, NSW 2010, Darlinghurst, Australia.
Bioinformatics. 2025 Mar 29;41(4). doi: 10.1093/bioinformatics/btaf151.
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.
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.
纳米孔测序仪可实现测序数据的实时获取。这使得在测序运行期间能够进行实时分析，从而缩短结果的周转时间。我们引入了realfreq，这是一个在纳米孔测序仪运行时获取实时碱基修饰频率的框架。Realfreq在测序仪运行时计算并允许访问实时碱基修饰频率结果。我们证明，在笔记本电脑上使用realfreq进行数据分析的速率能够跟上纳米孔MinION测序仪的输出数据速率，而台式计算机则能够跟上单个PromethION 2 solo流动槽的速率。
Realfreq是一个用C编程语言和 shell 脚本实现的免费开源应用程序。Realfreq的源代码和文档可在https://github.com/imsuneth/realfreq上找到。用于撰写本文的版本也可在https://doi.org/10.5281/zenodo.15128668上获取。
