---
name: "arden-create"
section: "1"
platform: "linux"
package: "arden"
version: "1.0-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/arden-create"
---

# arden-create(1)

generate an artificial reference genome (AR) from a given input

## NAME

arden-create - generate an artificial reference genome (AR) from a given input

## SYNOPSIS

**arden-create** \[*options*\] \[*OUTPUTFOLDER*\] \[*INPUT FASTA*\]...

## DESCRIPTION

Script to generate an artificial reference genome (AR) from a given input. The AR fulfills the following conditions by default settings:

- 1

  has a nucleotide distribution equal to the input genome

- 2

  has an amino acid (aa) distribution equal to the input genome

- 3

  keeps the aa neighborhood similar to the neighborhood in input genome

- 4

  protects start and stop codons from mutations

## OPTIONS

Required Arguments:

- *OUTPUTFOLDER*

  complete path to output destination folder

- *INPUT FASTA*

  Single sequence Fasta file.

-

  - **--version**

  show program's version number and exit

- **-h**, **--help**

  show this help message and exit

- **-d** DISTANCE, **--distance**=*DISTANCE*

  distance between 2 mutations on DNA level. The minimum distance will then be d-3. \[default: 15\]

- **-o** ORF, **--orf**=*ORF*

  1- protect ORF structure from mutations.   0 - allow mutations in start / stop codon \[default: 1\]

- **-r** REVSUB, **--revsub**=*REVSUB*

  1 - reverse substitution if no suitable counterpart was found (balanced mutation). 0 - keep the unbalanced mutations.\[default: 1\]

- **-m** RANDOM, **--random**=*RANDOM*

  1/0 variable. 1 - shuffled starting positions for the

-

  mutations. 0 - linear mutation \[default: 1\]

- **-s** SORF, **--saveorfs**=*SORF*

  Save found start and stop codons in a pickle file (can be loaded if the input fasta is used again if a filename is specified). \[default: \]

- **-l** LORF, **--loadorfs**=*LORF*

  Specify filename to a previously created pickle file (contains positions of start/stop codons) \[default: \]

- **-n** NAME, **--name**=*NAME*

  Specify name which will be used as header. \[default: \]

- **-p** PEXAMPLES, **--pexamples**=*PEXAMPLES*

  set to 1 if you want to print examples