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.
I am using nucmer from the mummer package (http://mummer.sourceforge.net/manual/) and trying to get the settings correct. I plan to use the tilings from nucmer -> show-tiling to construct the chromosome likely using biopython.
My questions are:
- Which settings for would be best for this task '-c' [min cluster] and '-l' [min match]? Is it safe (meaningful) to concatenate all scaffolds in order of the tiling from nucmer? Reverse complementing when needed of course.
- Are there any other programs designed to construct chromosomes from scaffolds given a reference? This seems like a routine/common task but I have not found much information on this specific problem.
- After constructing the new chromosome what is the best way to call SNPs?
Thanks!