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)

                                                                                REAPR-SMALTMAP(1)