RT Journal Article
SR Electronic
T1 What’s in my pot? Real-time species identification on the MinION™
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 030742
DO 10.1101/030742
A1 Sissel Juul
A1 Fernando Izquierdo
A1 Adam Hurst
A1 Xiaoguang Dai
A1 Amber Wright
A1 Eugene Kulesha
A1 Roger Pettett
A1 Daniel J. Turner
YR 2015
UL http://biorxiv.org/content/early/2015/11/06/030742.abstract
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.