PT  - JOURNAL ARTICLE
AU  - Sissel Juul
AU  - Fernando Izquierdo
AU  - Adam Hurst
AU  - Xiaoguang Dai
AU  - Amber Wright
AU  - Eugene Kulesha
AU  - Roger Pettett
AU  - Daniel J. Turner
TI  - What’s in my pot? Real-time species identification on the MinION™
AID  - 10.1101/030742
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 030742
4099  - http://biorxiv.org/content/early/2015/11/06/030742.short
4100  - http://biorxiv.org/content/early/2015/11/06/030742.full
AB  - 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.