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)