Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar. DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers. Technical Report bioRxiv:944223, Cold Spring Harbor Laboratory, February 2020.

Download preprint: not available

Download from publisher: https://doi.org/10.1101/2020.02.11.944223

Related web page: https://github.com/fmfi-compbio/deepnano-blitz

Bibliography entry: BibTeX


Motivation: Oxford 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.

Results: We 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).