Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 64,934 bioRxiv papers from 287,775 authors.

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

By Sissel Juul, Fernando Izquierdo, Adam Hurst, Xiaoguang Dai, Amber Wright, Eugene Kulesha, Roger Pettett, Daniel J Turner

Posted 06 Nov 2015
bioRxiv DOI: 10.1101/030742

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.

Download data

  • Downloaded 9,149 times
  • Download rankings, all-time:
    • Site-wide: 134 out of 64,934
    • In genomics: 42 out of 4,441
  • Year to date:
    • Site-wide: 1,688 out of 64,934
  • Since beginning of last month:
    • Site-wide: 3,877 out of 64,934

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News