I need to randomly shuffle genomes and check to see if they were indeed shuffled before proceeding. For the shuffle step, I've used EMBOSS shuffleseq.

The real question for me is how to check whether the genomes was shuffled randomly.

My questions are:

Q1. Can I use nucmer and simply count the number of lines in the output to figure out whether there are no real alignments to report

OR

Q2. If I should take it one step further and execute mummerplot on the .delta output from nucmer to see how it looks in postscript

Being new to mummer and mummerplot, I can generate png or ps images, but they are quite crude, and I think I am not using the correct filters in the nucmer step and the correct xrange and yrange in the mummerplot step, and IMHO the manual is not entirely helpful.

Q3. Are there good links that describe how to set/optimize parameters for mummer / nucmer / mummerplot?

Q4. I tried D-GENIES for pairwise genome alignments - which runs as an APACHE2 webserver on UBUNTU inside VirtualBox on my MacOSX machine, but I ran across RAM constraints for larger genomes, else that would have been an option.

And because I have 150 pairwise genome comparisons to make, with the genomes ranging in size from ~ 100Mb to ~ 2 GB, I am hoping your suggestion that will scale-up easily in batch mode, and on a LINUX-based compute cluster, and via command line (not GUI option). Thanks and HNY 2019 to all! :)