I have a de novo assembled mammalian genome (~300,000 contigs) that I want to align to a closely related existing reference genome using NUCmer from the MUMmer package. Subsequently, given the Coords output of the NUCmer alignment, I want to use something like OSLay to order and stitch together the contigs.
The problem is, NUCmer seems like it is going to take a very, very long time to run. I have split the reference genome up into single chromosomes and I am aligning all of my contigs to each chromosome (32 chromosomes, 32 jobs running at once). However, even the smallest chromosome has run over a day and is not complete. Any ideas on how to speed up the alignment?
nucmer --prefix bbu_vs_bt_ref_chr1 ./bt_ref_chr1.fa ./WB_2.0.fa