Competitive vs non-competitive mapping

[mcmahon-uw]

Hi, this is more of a question than an issue. I apologize if it's been asked before (I searched but didn't see much).

Are the mapping algorithms set up to be "competitive" in the sense that the software chooses which genome (contig) to assign the read, if there are multiple equally good match genomes (contigs)? And, is there a way to set them to be NOT COMPETITIVE (i.e. a read can map to more than one piece of reference sequence). I have reasons to run them either way. :-)

At the moment I'm just using the minimap2-sr default, but am happy to try another algorithm to make it work.

thank you! trina mcmahon