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

# arden-analyze(1)

analyze the results of the artificial reference genome mapping

## NAME

arden-analyze - analyze the results of the artificial reference genome mapping

## SYNOPSIS

**arden-analyze** \[*options*\] \[*INPUT FILE*\] \[*OUTPUTFOLDER*\] ...

## DESCRIPTION

Script to analyze the results of the artificial reference genome mapping. This script identifies the putative TPs / FPs on a specific data set (reads).

## OPTIONS

- *OUTPUTFOLDER*

  path to output destination folder.

- *INPUT FILE*

  ppath to ini file. To get the required format have a look at the example files.

- **--version**

  show program's version number and exit

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

  show this help message and exit

- **-p** PHRED, **--phred**=*PHRED*

  Specify the PHRED encoding of the input reads i.e. Illumina 1.3+ = **-p** 33.\[default: 33\]

- **-r** RANK, **--internalrank**=*RANK*

  Use internal ranking for reads (needed if the read names cannot be lexicographically be sorted in the same way in python and your OS by sam tools).\[default:1\]