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).