Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka.
Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.
Commun Biol. 2020 Sep 29;3(1):538. doi: 10.1038/s42003-020-01270-z.
The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.
便携式纳米孔测序设备的出现使得 DNA 和 RNA 测序能够在现场或临床进行。然而，原位基因组学的进步需要为测序数据的计算分析开发并行的便携式离线解决方案。在这里，我们介绍 Genopo，这是一个用于纳米孔测序分析的移动工具包。Genopo 将流行的生物信息学工具压缩到一个 Android 应用程序中，实现了完全便携式的计算。为了展示其在原位基因组分析中的实用性，我们使用 Genopo 从在纳米孔设备上测序的九个患者分离物中确定了人类冠状病毒 SARS-CoV-2 的完整基因组序列，Genopo 在一系列流行的智能手机上每个样本的执行时间不到 30 分钟。我们进一步展示了 Genopo 如何用于分析人类基因组样本中的 DNA 甲基化，说明了这种灵活、高效的架构适合运行许多流行的生物信息学工具，并适应小或大的基因组。作为首款用于纳米孔测序分析的智能手机应用程序，Genopo 使基因组学社区能够利用这种廉价、无处不在的计算资源。
