bionic (1) deepnano_basecall.1.gz

NAME

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

SYNOPSIS

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

DESCRIPTION

   positional arguments:
              reads

   optional arguments:
       -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

EXAMPLES

       For SQK-MAP-006 chemistry just use:
              OMP_NUM_THREADS=1 deepnano_basecall <list of fast5 files>

              or

              OMP_NUM_THREADS=1 deepnano_basecall --directory <directory with reads>

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

       For SQK-MAP-005 chemistry use:
              OMP_NUM_THREADS=1   deepnano_basecall   --template_net   nets_data/map5temp.npz   --complement_net
              nets_data/map5comp.npz --big_net nets_data/map5-2d.npz <list of fast5 files>

SEE ALSO

       deepnano_basecall_no_metrichor(1)

AUTHOR

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

BUGS

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