Man page - reapr-pipeline(1)

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Package: reapr
apt-get install reapr

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reapr

Manual

REAPR-PIPELINE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO

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.