deepnano_basecall_no_metrichor1
Basecaller for oxford nanopore minion reads based on deep recurrent neural networks
Usage
usage: deepnano_basecall_no_metrichor
[ARGS]
[reads
[reads ...]]
Overview
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> |
Releases
Unchanged in 2 releases since Debian 10 (Buster).