---
name: "reapr-pipeline"
section: "1"
platform: "linux"
package: "reapr"
version: "1.0.18+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/reapr-pipeline"
---

# reapr-pipeline(1)

run the REAPR pipeline

## NAME

reapr-pipeline - run the REAPR pipeline

## SYNOPSIS

**reapr pipeline** \[options\] \<assembly.fa\> \<in.bam\> \<outdirectory\> \[perfectmapprefix\]

## DESCRIPTION

\[perfectmapprefix\] is optional and should be the prefix used when task **perfectmap** was run.

It is assumed that reads in \<in.bam\> are 'innies', i.e. the correct orientation is reads in a pair pointing towards each other (--→ ←--).

## OPTIONS

**-stats\|fcdrate\|score\|break option=value**

You can pass options to **stats**, **fcdrate**, **score** or **break** if you want to change the default settings. These can be used multiple times to use more than one option. e.g.: **-stats i=100 -stats j=1000** If an option has no value, use **1**. e.g. **-break b=1**

- **-fcdcut** \<float\>

  Set the fcdcutoff used when running score. Default is to run fcdrate to determine the cutoff. Using this option will skip fcdrate and use the given value.

- **-x**

  By default, a bash script is written to run all the pipeline stages. Using this option stops the script from being run.

## SEE ALSO

[reapr(1)](/reapr/1.md)