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.\"     Title: reapr-break
.\"    Author: [see the "AUTHORS" section]
.\" Generator: Asciidoctor 1.5.4
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-BREAK" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr\-break \- make broken assembly via REAPR
.SH "SYNOPSIS"
.sp
\fBreapr break\fP [options] <assembly.fa> <errors.gff.gz> <outfileprefix>
.SH "DESCRIPTION"
.sp
<errors.gff.gz> is the errors GFF file made when running \fBscore\fP.
.SH "OPTIONS"
.sp
\fB\-a\fP
.RS 4
Aggressive breaking: break contigs at any FCD or low_frag error, as
opposed to the default of replacing with Ns. Contigs are broken at the
midpoint of each error. Also see option \fB\-t\fP. Incompatible with \fB\-b\fP.
.RE
.sp
\fB\-b\fP
.RS 4
Ignore FCD and low fragment coverage errors that do not contain
a gap (the default is to replace these with Ns). Incompatible with \fB\-a\fP.
.RE
.sp
\fB\-e\fP <float>
.RS 4
Minimum FCD error [0]
.RE
.sp
\fB\-l\fP <int>
.RS 4
Minimum sequence length to output [100]
.RE
.sp
\fB\-m\fP <int>
.RS 4
Max sequence length to write to the bin. Sequences longer
than this are written to the main assembly output. This is to stop
long stretches of sequence being lost [999]
.RE
.sp
\fB\-t\fP <int>
.RS 4
When \fB\-a\fP is used, use this option to specify how many bases
are trimmed off the end of each new contig around a break.
\fB\-t\fP N means that, at an FCD error, a contig is broken at the middle
coordinate of the error, then N bases are
trimmed off each new contig end [0]
.RE
.SH "SEE ALSO"
.sp
reapr(1)