NanoR: A user-friendly R package to analyze and compare nanopore sequencing data
NanoR: A user-friendly R package to analyze and compare nanopore sequencing data
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DOI：
10.1371/journal.pone.0216471
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发表时间：
2019-05-09
期刊：
影响因子：
3.7
通讯作者：
Magi, Alberto
中科院分区：
文献类型：
--
作者：
Bolognini, Davide;Bartalucci, Niccolo;Magi, Alberto
牛津纳米孔技术公司的MinION和GridION X5是用于实时DNA和RNA测序的设备。一方面，MinION是唯一的实时、低成本和便携式测序设备，由于其独特的性能，越来越受到生物学家的欢迎；另一方面，GridION X5，主要是因为它的成本，不太普遍，但非常适合有大型测序项目的研究人员。尽管牛津纳米孔技术公司的设备在过去几年中得到了越来越多的应用，但目前还缺乏高性能和用户友好的工具来处理MinION和GridION X5平台输出的数据。在这里，我们介绍了NanoR，一个跨平台的R包，旨在简化和改进纳米孔数据可视化。事实上，NanoR建立在几个功能上，但克服了现有工具从MinION测序数据中提取有意义信息的能力；此外，作为独家功能，NanoR可以处理GridION X5测序输出，并允许在一个命令中比较MinION和GridION X5测序数据。NanoR作为R的免费软件包发布在https://github.com/davidebolo1993/NanoR。
MinION and GridION X5 from Oxford Nanopore Technologies are devices for real-time DNA and RNA sequencing. On the one hand, MinION is the only real-time, low cost and portable sequencing device and, thanks to its unique properties, is becoming more and more popular among biologists; on the other, GridION X5, mainly for its costs, is less widespread but highly suitable for researchers with large sequencing projects. Despite the fact that Oxford Nanopore Technologies' devices have been increasingly used in the last few years, there is a lack of high-performing and user-friendly tools to handle the data outputted by both MinION and GridION X5 platforms. Here we present NanoR, a cross-platform R package designed with the purpose to simplify and improve nanopore data visualization. Indeed, NanoR is built on few functions but overcomes the capabilities of existing tools to extract meaningful informations from MinION sequencing data; in addition, as exclusive features, NanoR can deal with GridION X5 sequencing outputs and allows comparison of both MinION and GridION X5 sequencing data in one command. NanoR is released as free package for R at https://github.com/davidebolo1993/NanoR.