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>

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>

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