I am trying to use Mummer to differentiate core and accessory chromosomes in some genome assembly files I have. I used the following code to align single query file to the single reference file which seems to work fine.
nucmer -maxmatch -c 100 -p Fop Fol_fasta Fusox.fasta
But now I want to align multiple query assembly files to a single reference file, but nucmer gave me error on this. I also tried using just Mummer code like this:
mummer -maxmatch -b Necha.fasta Fsp.fasta Neo.fasta
but I don't get any output. I saw that in MUMmer manual they describe more about single query than multiple query files. Am I doing something wrong here. Could you please help.