Sequencing Nothing: Exploring Failure Modes of Nanopore Sensing and Implications for Life Detection

Using Oxford Nanopore Technologies MinION, we assess whether single molecule sequencing, involving no amplification, generates noise signals that could be misinterpreted in the context of a planetary exploration mission, and also whether the ability of the instrument to handle these types of situations could make it feasible for clean room monitoring. Utilizing the quality score filtering in place at the time of this experiment, runs containing only initial flowcell chemistry and/or library reagents generated 5 passing reads out of a total of 3,567 measured reads, and contained estimated sequences with low complexity that did not map to the NCBI database. The noise characteristics in all instances suggest that quality thresholds were appropriately chosen by ONT. New chemistry and basecalling workflows could further suppress noise sources, although this remains to be tested.