Workflow versatility: no fixed run time
A key feature of the MinION device, the PromethION and the GridION system is that there is no fixed run time; a user can run any of the systems for a short or long period of time as data is streamed in real time. This can enable real-time analyses so that the user can predetermine an experimental endpoint and run the system for as long as it takes to collect sufficient data to address that question.
During an experiment, each nanopore on the array sensor chip analyses molecules in the sample independently of the other nanopores. The shortest time to start collecting experimental data is the time taken for one analyte molecule to successfully interact with one nanopore in the array. This may be as quick as a few milliseconds for a single molecule like a protein. Or, in the case of polymers like DNA, a single molecule may take a period of time to pass through the nanopore, so dependent on fragment length, this first complete read may take milliseconds to seconds. During the run, each nanopore samples many analyte molecules from the surrounding solution, and additional complete reads are collected.
Data analysis takes place in real time as data streams from the sensor chip in parallel from multiple nanopores. Therefore, a longer run enables more data points to be collected, more confidence about an observation to be achieved, more measurement accuracy to be obtained, and a greater range of analyses to occur.
Run until... sufficient data
An Oxford Nanopore device may be instructed to Run until... a certain datum has been seen a certain number of times at a specified confidence level. In this way, the experiment is defined by the user, not defined by the machine. For example:
- DNA sequencing: the system may process the sample until a minimum of tenfold read coverage over specified regions of interest has been seen, until a specific mutation has been observed in a sample or until enough sequence data has been collected to reliably assemble a sample against a reference.
- Protein analysis: the system may process the sample until the presence of a specific analyte has been determined to a certain confidence level, and process the sample further to determine its concentration.
Real time analyses
Real time analyses can result in simpler workflows, for example the real time assembly of reads during an experiment.