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# reapr-smaltmap(1)
## NAME
reapr-smaltmap - map read pairs using SMALT
## SYNOPSIS
*reapr smaltmap* [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
## DESCRIPTION
Maps read pairs to an assembly with SMALT, making a final BAM file that
is sorted, indexed and has duplicates removed.
The n-th read in <reads_1.fastq> should be the mate of the n-th read in
<reads_2.fastq>.
It is assumed that reads are 'innies', i.e. the correct orientation
is reads in a pair pointing towards each other (---> <---).
## OPTIONS
*-k* <int>::
The -k option (kmer hash length) when indexing the genome
with 'smalt index' [13]
*-s* <int>::
The -s option (step length) when indexing the genome
with 'smalt index' [2]
*-m* <int>::
The -m option when mapping reads with 'smalt map' [not used by default]
*-n* <int>::
The number of threads used when running 'smalt map' [1]
*-y* <float>::
The -y option when mapping reads with 'smalt map'.
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]
*-x*::
Use this to just print the commands that will be run, instead of
actually running them
*-u* <int>::
The -u option of 'smalt sample'. This is used to estimate the insert
size from a sample of the reads, by mapping every n^th read pair [1000]
## SEE ALSO
reapr(1)
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