DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers

Abstract

MotivationOxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications. ResultsWe have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or pre-filtering of results for more detailed analysis (i.e. filtering out human DNA from human-pathogen runs). Availability and ImplementationDeepNano-blitz has been developed and tested on Linux and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz Contactvladimir.boza@fmph.uniba.sk