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What’s in my pot? Real-time species identification on the MinION™

Sissel Juul, Fernando Izquierdo, Adam Hurst, Xiaoguang Dai, Amber Wright, Eugene Kulesha, Roger Pettett, Daniel J. Turner
doi: https://doi.org/10.1101/030742
Sissel Juul
1Oxford Nanopore Technologies Inc., New York, USA
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Fernando Izquierdo
2Metrichor Ltd., Oxford, UK
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Adam Hurst
2Metrichor Ltd., Oxford, UK
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Xiaoguang Dai
1Oxford Nanopore Technologies Inc., New York, USA
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Amber Wright
2Metrichor Ltd., Oxford, UK
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Eugene Kulesha
2Metrichor Ltd., Oxford, UK
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Roger Pettett
2Metrichor Ltd., Oxford, UK
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Daniel J. Turner
3Oxford Nanopore Technologies Ltd., Oxford, UK
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  • For correspondence: daniel.turner@nanoporetech.com
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 06, 2015.
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What’s in my pot? Real-time species identification on the MinION™
Sissel Juul, Fernando Izquierdo, Adam Hurst, Xiaoguang Dai, Amber Wright, Eugene Kulesha, Roger Pettett, Daniel J. Turner
bioRxiv 030742; doi: https://doi.org/10.1101/030742
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What’s in my pot? Real-time species identification on the MinION™
Sissel Juul, Fernando Izquierdo, Adam Hurst, Xiaoguang Dai, Amber Wright, Eugene Kulesha, Roger Pettett, Daniel J. Turner
bioRxiv 030742; doi: https://doi.org/10.1101/030742

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