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

Bioinformatics (Oxford, England) Pub Date : 2025-03-29 DOI:10.1093/bioinformatics/btaf151

Suneth Samarasinghe, Ira Deveson, Hasindu Gamaarachchi

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Abstract

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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Realfreq：用于纳米孔测序的实时碱基修饰分析。

摘要：纳米孔测序仪允许实时访问测序数据。这允许在测序运行时执行实时分析，减少结果的周转时间。我们介绍了realfreq，这是一个在纳米孔测序器工作时获得实时碱基修饰频率的框架。Realfreq计算并允许访问实时碱基修改频率结果，而测序器正在运行。我们证明了在笔记本电脑上使用realfrequency的数据分析速率可以跟上纳米孔MinION测序仪的输出数据速率，而台式电脑可以跟上单个PromethION 2单独流动池的输出数据速率。可用性和实现：Realfreq是一个免费的开源应用程序，使用C语言和shell脚本实现。realfreq的源代码和文档可以在https://github.com/imsuneth/realfreq上找到。手稿使用的版本也可在10.5281/zenodo.15128668处获得。补充信息：补充数据可在生物信息学在线获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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