'\" t
.\"     Title: reapr-perfectmap
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-PERFECTMAP" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\fI\\$2\fP <\\$1>\\$3
..
.als MTO URL
.if \n[.g] \{\
.  mso www.tmac
.  am URL
.    ad l
.  .
.  am MTO
.    ad l
.  .
.  LINKSTYLE blue R < >
.\}
.SH "NAME"
reapr-perfectmap \- make perfect uniquely mapping plot files
.SH "SYNOPSIS"
.sp
\fBreapr perfectmap\fP <assembly.fa> <reads_1.fastq> <reads_2.fastq> <avginsertsize> <outprefix>
.SH "DESCRIPTION"
.sp
Note: the reads can be gzipped.  If the extension is \*(Aq.gz\*(Aq, then they
are assumed to be gzipped and dealt with accordingly (i.e. called something
like <reads_1.fastq.gz> <reads_2.fastq.gz>).
.if n .sp
.RS 4
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
.B Important
.ps -1
.br
.sp
all reads must be the same length.
.sp .5v
.RE
.SH "SEE ALSO"
.sp
reapr(1)