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# reapr-pipeline(1)
## NAME
reapr-pipeline - run the REAPR pipeline
## SYNOPSIS
*reapr pipeline* [options] <assembly.fa> <in.bam> <outdirectory> [perfectmapprefix]
## DESCRIPTION
[perfectmapprefix] is optional and should be the prefix used when task
*perfectmap* was run.
It is assumed that reads in <in.bam> are 'innies', i.e. the correct orientation
is reads in a pair pointing towards each other (---> <---).
## OPTIONS
*-stats|fcdrate|score|break option=value*::
You can pass options to *stats*, *fcdrate*, *score* or *break*
if you want to change the default settings. These
can be used multiple times to use more than one option. e.g.:
*-stats i=100 -stats j=1000*
If an option has no value, use *1*. e.g.
*-break b=1*
*-fcdcut* <float>::
Set the fcdcutoff used when running score. Default is to
run fcdrate to determine the cutoff. Using this option will
skip fcdrate and use the given value.
*-x*::
By default, a bash script is written to run all
the pipeline stages. Using this option stops the
script from being run.
## SEE ALSO
reapr(1)
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