= reapr(1)

== 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-smaltmap(1), reapr-perfectmap(1), reapr-pipeline(1), reapr-plots(1), reapr-seqrename(1), reapr-preprocess(1), reapr-stats(1), reapr-fcdrate(1), reapr-score(1), reapr-summary(1), reapr-break(1), reapr-gapresize(1), reapr-perfectfrombam(1)
