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

# reapr(1)

universal tool for genome assembly evaluation

## NAME

reapr - universal tool for genome assembly evaluation

## SYNOPSIS

**reapr** \<task\> \[options\]

## DESCRIPTION

reapr is the main executable for the **REAPR** software. The actual functionality is provided by the subtools (\*tasks'):

### Common tasks

**facheck**

checks IDs in fasta file

**smaltmap**

map read pairs using SMALT: makes a BAM file to be used as input to the pipeline

**perfectmap**

make perfect uniquely mapping plot files

**pipeline**

runs the REAPR pipeline, using an assembly and mapped reads as input, and optionally results of perfectmap. (It runs facheck, preprocess, stats, fcdrate, score, summary and break)

**plots**

makes Artemis plot files for a given contig, using results from stats (and optionally results from score)

**seqrename**

renames all sequences in a BAM file: use this if you already mapped your reads but then found facheck failed - saves remapping the reads so that pipeline can be run

### Advanced tasks

**preprocess**

preprocess files: necessary for running stats

**stats**

generates stats from a BAM file

**fcdrate**

estimates FCD cutoff for score, using results from stats

**score**

calculates scores and assembly errors, using results from stats

**summary**

make summary stats file, using results from score

**break**

makes broken assembly, using results from score

**gapresize**

experimental, calculates gap sizes based on read mapping

**perfectfrombam**

generate perfect mapping plots from a bam file (alternative to using perfectmap for large genomes)

## SEE ALSO

[reapr-facheck(1)](/reapr-facheck/1.md), [reapr-smaltmap(1)](/reapr-smaltmap/1.md), [reapr-perfectmap(1)](/reapr-perfectmap/1.md), [reapr-pipeline(1)](/reapr-pipeline/1.md), [reapr-plots(1)](/reapr-plots/1.md), [reapr-seqrename(1)](/reapr-seqrename/1.md), [reapr-preprocess(1)](/reapr-preprocess/1.md), [reapr-stats(1)](/reapr-stats/1.md), reapr-fcdrate(1), [reapr-score(1)](/reapr-score/1.md), [reapr-summary(1)](/reapr-summary/1.md), [reapr-break(1)](/reapr-break/1.md), [reapr-gapresize(1)](/reapr-gapresize/1.md), [reapr-perfectfrombam(1)](/reapr-perfectfrombam/1.md)