I'm using fastq screen to check some files. It runs fine, but I noticed that when using bwa as aligner it defaults to bwa mem, as mentioned in the docs for the --aligner parameter
... BWA with mem -a
As I have 42bp SE reads I'd rather use bwa aln, which isn't mentioned anywhere in the docs, so I was wondering if there's a way to hack this default and instruct fastq screen to use aln and not mem. I tried to play with the parameter
bwa "<"text">" : Specify extra parameters to be passed to BWA
but I don't seem to get an acceptable syntax.
Does anyone know whether this
1) is possible at all
2) if yes, how to do it?