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

# reapr-score(1)

calculate scores and assembly errors

## NAME

reapr-score - calculate scores and assembly errors

## SYNOPSIS

**reapr score** \[options\] \<assembly.fa.gaps.gz\> \<in.bam\> \<statsprefix\> \<FCDcutoff\> \<outprefix\>

## OPTIONS

- **-f** \<int\>

  Minimum inner fragment coverage \[1\]

- **-g** \<int\>

  Max gap length to call over \[0.5 \* outer\_mean\_insert\_size\]

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

  Length of window \[100\]

- **-p** \<int\>

  Use perfect mapping reads score with given min coverage. Incompatible with -P.

- **-P** \<int\>

  Same as -p, but force the score to be zero at any position with at least the given coverage of perfect mapping reads and which has an OK insert plot, , i.e. perfect mapping reads + insert distribution override all other tests when calculating the score. Incompatible with -p.

- **-q** \<float\>

  Max bad read ratio \[0.33\]

- **-r** \<int\>

  Min read coverage \[max(1, mean\_read\_cov - 4 \* read\_cov\_stddev)\]

- **-R** \<int\>

  Repeat calling cutoff. -R N means call a repeat if fragment coverage is \>= N times (expected coverage). Use -R 0 to not call repeats \[2\]

- **-s** \<int\>

  Min score to report in errors file \[0.4\]

- **-u** \<int\>

  FCD error window length for error calling \[insert\_size / 2\]

- **-w** \<float\>

  Min percentage of bases in window needed to call as bad \[0.8\]

## SEE ALSO

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