reapr-smaltmap - map read pairs using SMALT
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 (--→
←--).
-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]