Is there an aligner that allows me to ignore reverse complement alignments. For example, my reference sequence I'm aligning to will always be single stranded sense DNA (the antisense strand is selectivily degraded). Also, the fragments I'm aligning are always going to be single stranded sense DNA strands. I was using BWA but there doesn't seem to be an option to ignore reverse complement alignments. Does any aligner out there do this? Thanks!
Bowtie seems to be able to do it with this parameter:
--nofw/--norc If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. For paired-end reads using --fr or --rf modes, --nofw and --norc apply to the forward and reverse-complement pair orientations. I.e. specifying --nofw and --fr will only find reads in the R/F orientation where mate 2 occurs upstream of mate 1 with respect to the forward reference strand.