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