DeepNano-blitz: a fast base caller for MinION nanopore sequencers.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 32374816.
- Also identified by DOI 10.1093/bioinformatics/btaa297.
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Abstract
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. 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 prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human-pathogen runs). DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz. vladimir.boza@fmph.uniba.sk. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Nanopores