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)