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| 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 |