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

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.

Beyond Homopolymer Errors: a Systematic Investigation of Nanopore-based DNA Sequencing Characteristics Using HLA-DQA2

“…This opens up an array of opportunities in the field of metagenomics and pathogen identification, particularly with the feasibility of portable sequencing [17,18]. PCR-free library preparation techniques offer quantitative and qualitative cancer profiling, immunome profiling and mtDNA profiling.…”

MetaGenomic analysis of short and long reads

“…Strikingly, the study, which produced the in vitro reads (Cuscó et al 2018), used the WIMP workflow which was published specifically for the MinION (Juul et al 2015). Thus, MetaG is powerful enough to beat algorithms at their own game.…”

“…After the promising results from the previous analyses, we reanalyzed genuine Nanopore sequences from a bacterial community with a known abundance distribution. The data generated by Cuscó and coworkers had been previously analyzed by the authors using the Nanopore specific What's in my Pot (WIMP) workflow (Cuscó et al 2018;Juul et al 2015).…”

Genomics in the jungle: using portable sequencing as a teaching tool in field courses

“…In addition, we ran a blank sample to control for possible contamination during extractions and PCRs. Bioinformatic analyses were carried out using ONT's WIMP software (Juul et al, 2015). For PCR conditions and a full protocol see Protocols.io .…”

“…The fewest reads (state reads) were unfortunately obtained from the flowcell running the 16s and 18s metagenomics libraries. However, subsequent pilot analyses on WIMP (Juul et al, 2015) indicated some success, but coverage overlap is yet to be assessed.…”