Man pages sections > man1 > deepnano_basecall

deepnano_basecall - basecaller for Oxford Nanopore MinION reads based on deep

DEEPNANO_BASECALL(1) User Commands DEEPNANO_BASECALL(1)

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>
 
February 2017 deepnano_basecall 0.0+20110617