Metagenomics Analysis & Species Identification
The portable nanopore MinION is now being used for rapid environmental and metagnemoic analyses and species identification in the field.
How is the MinION being used in for environmental or metagenomic analyses?
- Metagenomic analysis of complex samples including environmental or biological samples, e.g. Australia’s pink lake, infection control (or pathogen detection), microbiomes and more
- Discovery (or identification) of new nitrogen fixing bacteria
- Species taxonomy and relative abundance studies e.g. WIMP or 16S, CO1, and ITS
- Microbiome analysis
- Any DNA/RNA analysis in remote locations e.g. in the jungle, on a river bed, at a local clinic in a rural area
- Many tools are in development to allow real time metagenomic analysis during a MinION run
If you are looking for a rapid turnaround of data with real-time analysis, long read lengths and a portable system that can be used in remote environments...
Nanopore sequencing on the MinION gives you:
Efficient genome assembly and rapid species identification
The Oxford Nanopore system processes the library strands that are presented to it, regardless of their length, rather than generating reads of a specific length. Users can choose long reads of several kilobases to ultra-long reads of hundreds of kilobases, which are beneficial for metagenomic assembly. Long reads also aid rapid and unambiguous identification and quantification of species present within complex samples.Publications on long reads
Real-time data, rapid results
Nanopore sequencing data starts streaming immediately, rather than being delivered in bulk at the end of a 'run'. Real-time data streaming allows immediate analysis of this data, enabling users to perform assembly and mapping / alignment during the experiment. Rapid identification of organisms in the sample is also possible using a number of tools. Oxford Nanopore provides a dedicated workflow 'WIMP: Bacteria, Virus, Fungi and Archaea', which gives real-time species identification and characterisation. Further workflows in development will enable species identification based on barcode of life sequence clusters, or the presence of antimicrobial markers in pathogens within a sample.Publications on rapid identification
Preparation of sequencing libraries from genomic DNA is simple, and takes about ten minutes with the latest kit. Oxford Nanopore is developing new devices to simplify this even further.
Real-time data analysis means that workflows can be streamlined: sequencing can be stopped when an answer is been reached – perhaps a specific species has been identified in your sample – allowing you to move on to the next experiment.Publications on simple workflow
The MinION weighs under 100g and can fit in a pocket. It is powered by the USB port on a laptop and is uniquely transportable into the field. With library preparation possible using only a minimum of equipment, field-based analysis labs have been setup in remote destinations. Oxford Nanopore is also preparing to release automated sample and library preparation devices to simplify the workflow even further.Publications on transportable labs
How are others using the MinION for metagenomics and mobile analyses? What tools are available?
View these publications and movies to find out more.
Oxford Nanopore MinION Applications: Kits and tools, genetics and metagenomics
Dr Dan Turner
What's in my pot (WIMP)
'What's in my pot' (WIMP) is a workflow that enables MinION users to identify bacteria, fungi, viruses or archea in complex samples in real time.
Analysis begins as soon as sequence data starts being streamed (a few seconds after the experiment starts). Each read of streamed sequence data is compared against a database of microbial species, and an identification is made. At the same time, WIMP plots and updates a taxonomic tree of all microorganisms found in the sample.
There are various workflows and techniques that have been developed by members of the nanopore community to perform or enhance assembly and species identification that can be explored in the publications area and within the nanopore community.
How do I get started?
You can start using MinION straight away.
For a $1,000 fee you receive a MinION and starter pack of flow cells and kits. You also get access to a thriving online community of MinION users.