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

# reapr-perfectmap(1)

make perfect uniquely mapping plot files

## NAME

reapr-perfectmap - make perfect uniquely mapping plot files

## SYNOPSIS

**reapr perfectmap** \<assembly.fa\> \<reads\_1.fastq\> \<reads\_2.fastq\> \<avginsertsize\> \<outprefix\>

## DESCRIPTION

Note: the reads can be gzipped.  If the extension is '.gz', then they are assumed to be gzipped and dealt with accordingly (i.e. called something like \<reads\_1.fastq.gz\> \<reads\_2.fastq.gz\>).

**Important**\

all reads must be the same length.

## SEE ALSO

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