Marini Simone, Barquero Alexander, Wadhwani Anisha Ashok, Bian Jiang, Ruiz Jaime, Boucher Christina, Prosperi Mattia
Department of Epidemiology, University of Florida, Gainesville, USA.
Emerging Pathogens Institute, University of Florida, Gainesville, USA.
AMIA Annu Symp Proc. 2025 May 22;2024:798-807. eCollection 2024.
Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in clinical and environmental health. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. Here we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases, making it ideal for running on smartphones or tablets. OCTOPUS obtains sensitivity and precision comparable to Kraken2, while dramatically decreasing (4- to 16-fold) the false positive rate, and yielding high correlation on real-word data. OCTOPUS is available along with customized databases at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.
诸如牛津纳米孔公司的MinION这类便携式基因组测序仪能够在临床和环境卫生领域实现实时应用。然而，当生物信息学流程不可用时，例如由于没有网络连接而无法进行云处理，或者现场只能携带低端计算设备时，下游分析就会出现瓶颈。在此，我们展示了一款便于在平台上运行的软件，用于对纳米孔数据进行便携式宏基因组分析，即通过单例进行分类操作和泛基因组单元的基于寡聚体的分类器（OCTOPUS）。OCTOPUS用Java编写，重新实现了流行软件Kraken2和KrakenUniq的若干功能，并具有用于在不完整/抽样参考数据库上改进宏基因组学分类的原创组件，使其非常适合在智能手机或平板电脑上运行。OCTOPUS获得了与Kraken2相当的灵敏度和精度，同时大幅降低（4至16倍）了误报报率率，并在实际数据上产生了高度相关性。OCTOPUS以及定制数据库可在https://github.com/DataIntellSystLab/OCTOPUS和https://github.com/Ruiz-HCI-Lab/OctopusMobile上获取。
