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

# reapr-break(1)

make broken assembly via REAPR

## NAME

reapr-break - make broken assembly via REAPR

## SYNOPSIS

**reapr break** \[options\] \<assembly.fa\> \<errors.gff.gz\> \<outfileprefix\>

## DESCRIPTION

\<errors.gff.gz\> is the errors GFF file made when running **score**.

## OPTIONS

- **-a**

  Aggressive breaking: break contigs at any FCD or low\_frag error, as opposed to the default of replacing with Ns. Contigs are broken at the midpoint of each error. Also see option **-t**. Incompatible with **-b**.

- **-b**

  Ignore FCD and low fragment coverage errors that do not contain a gap (the default is to replace these with Ns). Incompatible with **-a**.

- **-e** \<float\>

  Minimum FCD error \[0\]

- **-l** \<int\>

  Minimum sequence length to output \[100\]

- **-m** \<int\>

  Max sequence length to write to the bin. Sequences longer than this are written to the main assembly output. This is to stop long stretches of sequence being lost \[999\]

- **-t** \<int\>

  When **-a** is used, use this option to specify how many bases are trimmed off the end of each new contig around a break. **-t** N means that, at an FCD error, a contig is broken at the middle coordinate of the error, then N bases are trimmed off each new contig end \[0\]

## SEE ALSO

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