I would like to know your thoughts about comperative genomics.
I have two assemblies (reference and draft) of the same species, a worm species. I wanted to compare scaffolds orders in the assemblies. I first used Mauve for alignment and later "move contig order" of Mauve program. Mauve reordered scaffolds of draft assembly, but I checked scaffolds of the draft assembly and I noticed that the reordering is not well done. For instance, I was expecting replace of scaffolds, matched with scaffolds of the reference assembly, after reordering. I mean scaffold 116, 422, 1038 of the draft assembly matched with scaffold 1 of the reference assembly. Therefore, I was expecting replace scaffold 116 as the first scaffold of the draft assembly.
I also run blast, and blast found different matching from Mauve.
My question is which results should I use? Mauve or Blast?
Or should I check each order of scaffolds of the draft assembly one by one and reorder these scaffolds by extracting their sequences, which will be a very time consuming process I think.