reapr smaltmap [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
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 (--→ ←--).
- The -k option (kmer hash length) when indexing the genome with 'smalt index' 
The -s option (step length) when indexing the genome
with 'smalt index' 
- The -m option when mapping reads with 'smalt map' [not used by default]
- The number of threads used when running 'smalt map' 
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]
Use this to just print the commands that will be run, instead of actually running them
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