Man pages sections > man1 > deepnano_basecall_no_metrichor

deepnano_basecall_no_metrichor - basecaller for Oxford Nanopore MinION reads

DEEPNANO_BASECALL_NO_METRICHOR(1) User Commands DEEPNANO_BASECALL_NO_METRICHOR(1)

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>
 
February 2017 deepnano_basecall_no_metrichor 0.0+20110617