---
name: "deepnano_basecall"
section: "1"
platform: "linux"
package: "deepnano"
version: "0.0+git20170813.e8a621e-3.1"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/deepnano_basecall"
---

# deepnano\_basecall(1)

basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks

## 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)](/deepnano_basecall_no_metrichor/1.md)

## 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\>