'\" t
.\"     Title: reapr-smaltmap
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 1.5.7.1
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-SMALTMAP" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr\-smaltmap \- map read pairs using SMALT
.SH "SYNOPSIS"
.sp
\fBreapr smaltmap\fP [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
.SH "DESCRIPTION"
.sp
Maps read pairs to an assembly with SMALT, making a final BAM file that
is sorted, indexed and has duplicates removed.
.sp
The n\-th read in <reads_1.fastq> should be the mate of the n\-th read in
<reads_2.fastq>.
.sp
It is assumed that reads are \(aqinnies\(aq, i.e. the correct orientation
is reads in a pair pointing towards each other (\-\-\(-> \(<-\-\-).
.SH "OPTIONS"
.sp
\fB\-k\fP <int>
.RS 4
The \-k option (kmer hash length) when indexing the genome
with \(aqsmalt index\(aq [13]
.RE
.sp
\fB\-s\fP <int>
.RS 4
The \-s option (step length) when indexing the genome
 with \(aqsmalt index\(aq [2]
.RE
.sp
\fB\-m\fP <int>
.RS 4
The \-m option when mapping reads with \(aqsmalt map\(aq [not used by default]
.RE
.sp
\fB\-n\fP <int>
.RS 4
The number of threads used when running \(aqsmalt map\(aq [1]
.RE
.sp
\fB\-y\fP <float>
.RS 4
  The \-y option when mapping reads with \(aqsmalt map\(aq.
The default of 0.5 means that at least 50% of each read must map
perfectly. Depending on the quality of your reads, you may want to
increase this to be more stringent (or consider using \-m) [0.5]
.RE
.sp
\fB\-x\fP
.RS 4
  Use this to just print the commands that will be run, instead of
actually running them
.RE
.sp
\fB\-u\fP <int>
.RS 4
    The \-u option of \(aqsmalt sample\(aq. This is used to estimate the insert
size from a sample of the reads, by mapping every n^th read pair [1000]
.RE
.SH "SEE ALSO"
.sp
reapr(1)