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DeepNano specifications


Unique identifier OMICS_14561
Name DeepNano
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Oxford Nanopore MinION reads
Output data Basecalls for template, complement and 2D into file
Output format FASTA
Biological technology Oxford Nanopore
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Cython, numpy, h5py, Theano, Python-dateutil
Maintained Yes




No version available



  • person_outline Vladimir Boza
  • person_outline Tomas Vinar

Publication for DeepNano

DeepNano citation


Scaffolding and completing genome assemblies in real time with nanopore sequencing

Nat Commun
PMCID: 5321748
PMID: 28218240
DOI: 10.1038/ncomms14515

[…] from the sequencer and report the current status of the analysis in real-time. our pipeline still relies on a base-caller, and the introduction of fast real-time base-callers such as nanocall and deepnano helps to reduce the latency. the current pipeline processes a sequence read within minutes of it finishing traversing the pore, rather than as the read is actually passing through the pore, […]

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DeepNano institution(s)
Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
DeepNano funding source(s)
Supported by VEGA grants 1/0684/16 and 1/0719/14, and a grant from the Slovak Research and Development Agency APVV-14-0253.

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