[MUMmer-help] Aligning a 30 Mb scaffold to a 3 Gb Reference

[Sanjit S. B. <san...@gm...>]

Hey!

I have a 30Mb scaffold that was assembled using optical maps. I would like
to align it to a 3Gb long reference assembly. Given the method through
which this scaffold was constructed, it should align to a region in the
reference, roughly the same size as itself.

I am currently running nucmer with the -c 100 flag, and I get a very large
number of fragmented alignments, the longest of which is under 1Mb. Is
there any way I can alter the flags to get a larger, less fragmented
alignment, for this particular case?

Any suggestions are appreciated. Thanks!