deepnano_basecall_no_metrichor(1)

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

NAME

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

SYNOPSIS

usage: deepnano_basecall_no_metrichor [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)

--max_2d_length MAX_2D_LENGTH: Max length for 2d basecall

--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

--directory DIRECTORY: Directory where read files are stored

--watch WATCH: Watched directory

EXAMPLES

Using without metrichor:: OMP_NUM_THREADS=1 deepnano_basecall_no_metrichor <list of fast5 files>

If you want to watch a directory (watchdog must be installed): OMP_NUM_THREADS=1 deepnano_basecall_no_metrichor --watch <directory name>

SEE ALSO

deepnano_basecall(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>