I want to use bwa mem or aln, to align reads to 3-5 strains of a virus. However, if a read can map with equal quality/score to more than 1 strain, i want the read to be reported as unaligned. Basically, only reads that map to one strain only with a best score should be considered.
The genomes of the 5 strains are in a fasta file, each genome is present in one DNA molecule. The tricky part, is that vaccinia viruses have IR at the 3' and 5' ends of their genomes, so this is a repetitive regions within one strain.
What approach would you guys recommend? For sampe and samse I see the -n option can be set to 1 to accomplish what I need, but that might also mean that IR regions will not have mappings.