reapr-smaltmap1
Map read pairs using smalt
Usage
reapr smaltmap
[options]
<assembly.fa>
<reads_1.fastq>
<reads_2.fastq>
<out.bam>
Overview
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]
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.