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.\"     Title: reapr
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr \- universal tool for genome assembly evaluation
.SH "SYNOPSIS"
.sp
\fBreapr\fP <task> [options]
.SH "DESCRIPTION"
.sp
reapr is the main executable for the \fBREAPR\fP software. The actual
functionality is provided by the subtools (*tasks\*(Aq):
.SS "Common tasks"
.sp
\fBfacheck\fP
.RS 4
checks IDs in fasta file
.RE
.sp
\fBsmaltmap\fP
.RS 4
map read pairs using SMALT: makes a BAM file to be used as input to the pipeline
.RE
.sp
\fBperfectmap\fP
.RS 4
make perfect uniquely mapping plot files
.RE
.sp
\fBpipeline\fP
.RS 4
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)
.RE
.sp
\fBplots\fP
.RS 4
makes Artemis plot files for a given contig, using results from stats (and optionally results from score)
.RE
.sp
\fBseqrename\fP
.RS 4
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
.RE
.SS "Advanced tasks"
.sp
\fBpreprocess\fP
.RS 4
preprocess files: necessary for running stats
.RE
.sp
\fBstats\fP
.RS 4
generates stats from a BAM file
.RE
.sp
\fBfcdrate\fP
.RS 4
estimates FCD cutoff for score, using results from stats
.RE
.sp
\fBscore\fP
.RS 4
calculates scores and assembly errors, using results from stats
.RE
.sp
\fBsummary\fP
.RS 4
make summary stats file, using results from score
.RE
.sp
\fBbreak\fP
.RS 4
makes broken assembly, using results from score
.RE
.sp
\fBgapresize\fP
.RS 4
experimental, calculates gap sizes based on read mapping
.RE
.sp
\fBperfectfrombam\fP
.RS 4
generate perfect mapping plots from a bam file (alternative to using perfectmap for large genomes)
.RE
.SH "SEE ALSO"
.sp
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)