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)

                                                                                                        REAPR(1)