What’s in my pot? Real-time species identification on the MinION™
What’s in my pot? Real-time species identification on the MinION™
复制标题
MinION™ 实时识别我的花盆里有什么？
DOI：
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
D. Turner
中科院分区：
文献类型：
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作者：
S. Juul;F. Izquierdo;Adam Hurst;Xiaoguang Dai;A. Wright;Eugene Kulesha;Roger Pettett;D. Turner
下一代仪器上的全基因组测序提供了一种公正的方法来鉴定复杂宏基因组样品中存在的生物体。然而，由于固定时间的测序运行和繁琐的生物信息学工作流程，获得结果的时间可能会延长。这限制了该方法在快速物种鉴定至关重要的环境中的实用性，例如在食物链组成部分的质量控制中，或在传染病爆发期间。在这里，我们提出什么是在我的锅？WIMP是一种实验室和分析工作流程，其中从未处理的样品开始，在大约3.5小时内生成序列数据，并将样品中存在的细菌、病毒和真菌以定量方式分类为亚种和菌株水平，而无需事先了解样品组成。该工作流程依赖于Oxford Nanopore Technologies的MinION™传感设备与实时物种识别生物信息学应用程序的组合。
Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows. This limits the utility of the approach in settings where rapid species identification is crucial, such as in the quality control of food-chain components, or in during an outbreak of an infectious disease. Here we present What’s in my Pot? (WIMP), a laboratory and analysis workflow in which, starting with an unprocessed sample, sequence data is generated and bacteria, viruses and fungi present in the sample are classified to subspecies and strain level in a quantitative manner, without prior knowledge of the sample composition, in approximately 3.5 hours. This workflow relies on the combination of Oxford Nanopore Technologies’ MinION™ sensing device with a real-time species identification bioinformatics application.