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) REAPR(1)
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