Hi, I have a genome of a wild plant subspecies in the form of about 200K scaffolds of various sizes from a few thousand bp to over 50kb. I am trying to assemble these into chromosomes using the the chromosome sequences of the nearest domesticated relative.
Ultimately I went with Lastz for the alignment from this paper's supplements. They aligned closely related rhesus species. The lastz process was very time consuming taking over a week for some of the chromosomes. But I guess its better to get it right.
This is the command I ended up using.
lastz Chr01.fasta scaffolds.fasta M=254 K=4500 L=3000 Y=15000 C=2 T=2 --format=axt > chr1.axt