deepnano_basecall - basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks

       This manpage was written by Çağrı ULAŞ for the Debian distribution and can be used for any other usage of
       the program.

       Report bugs to <https://bitbucket.org/vboza/deepnano/issues>

deepnano_basecall 0.0+20110617                    February 2017                             DEEPNANO_BASECALL(1)

positionalarguments:
              reads

   optionalarguments:-h, --help
              show this help message and exit

       --template_net TEMPLATE_NET
              path to network which basecalls template (has reasonable default)

       --complement_net COMPLEMENT_NET
              path to network which basecalls complement (has reasonable default)

       --big_net BIG_NET
              path to network which basecalls 2D (has reasonable default)

       --timing
              if set, display timing information for each read

       --type TYPE
              One   of:   template,   complement,  2d,  all,  use  comma  to  separate  multiple  options,  eg.:
              template,complement type of basecalling output (defaults to all)

       --output OUTPUT
              output filename

       --output_orig
              if set, outputs also Metrichor basecalls

       --directory DIRECTORY
              Directory where read files are stored

       For SQK-MAP-006 chemistry just use:
              OMP_NUM_THREADS=1deepnano_basecall<listoffast5files>

              or

              OMP_NUM_THREADS=1deepnano_basecall--directory<directorywithreads>

              It outputs basecalls for template, complement and 2D into file named output.fasta.

       For SQK-MAP-005 chemistry use:
              OMP_NUM_THREADS=1deepnano_basecall--template_netnets_data/map5temp.npz--complement_netnets_data/map5comp.npz--big_netnets_data/map5-2d.npz<listoffast5files>

       deepnano_basecall - basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks

deepnano_basecall_no_metrichor(1)

usage: deepnano_basecall [ARGS] [reads [reads ...]]