Investigate performance with big k-mer sizes (e.g. 5,001) #22
Description
Example: when creating the dot plot of two ~5 Mbp genomes using k = 5,001, the common substrings method runs out of memory (despite it handling k = 33 for the same sequences fine). Not sure why exactly.
However, the "suff-only" method can actually handle this okay.
It would be nice to have some guidance on why big k-mer sizes cause problems, and how to handle them. I am not sure if anyone is out here regularly creating dot plots with k-mer sizes in the thousands and up, but apparently this tool can do that at least :)