| 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¶
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 |