---
name: "ragout"
section: "1"
platform: "linux"
package: "ragout"
version: "2.3-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ragout"
---

# ragout(1)

Chromosome assembly with multiple references

## NAME

ragout - Chromosome assembly with multiple references

## SYNOPSIS

**ragout** \[-h\] \[-o output\_dir\] \[-s {sibelia,maf,hal}\] \[--refine\] \[--solid-scaffolds\] \[--overwrite\] \[--repeats\] \[--debug\] \[-t THREADS\] \[--version\] recipe\_file

## OPTIONS

### positional arguments:

- recipe\_file

  path to recipe file

### optional arguments:

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

  show this help message and exit

- **-o** output\_dir, **--outdir** output\_dir

  output directory (default: ragout-out)

- **-s** {sibelia,maf,hal}, **--synteny** {sibelia,maf,hal}

  backend for synteny block decomposition (default: sibelia)

- **--refine**

  enable refinement with assembly graph (default: False)

- **--solid-scaffolds**

  do not break input sequences - disables chimera detection module (default: False)

- **--overwrite**

  overwrite results from the previous run (default: False)

- **--repeats**

  enable repeat resolution algorithm (default: False)

- **--debug**

  enable debug output (default: False)

- **-t** THREADS, **--threads** THREADS

  number of threads for synteny backend (default: 1)

- **--version**

  show program's version number and exit

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.