Running and Reading in Real Time - Looking at Squiggles on the Oxford Nanopore MinION

The utility of the Oxford nanopore MinION sequencer is becoming clear. However, to fully exploit its potential requires a shift in thought in both experimental design and analysis. The conventional model of sequence, map and analysis leading to final result has been replaced by instant access to sequence data before the completion of a sequencing run. In the extreme case of the ONT MinION it is possible to analyse squiggle data before a read has even completed. We have developed a platform of tools, minoTour, to analyse MinION data in real time and extend it to exploit both ‘Run Until’ and, in future, ‘Read Until’. Run until allows the sequencer to switch off after achieving a specific goal, such as depth of coverage. Read until allows individual reads to be rejected from the pore and free that pore to sequence an alternative preferred read. We have developed method for run and read until in a number of different scenarios including selective small genome sequencing on barcode normalization. Limitations and challenges to implementing read until will be discussed along with the challenge of Fast Mode whereby speed of processing will be of vital importance. Finally we demonstrate how methodologies for analysing squiggles may help to reduce the reliance on base calling in the field.