Sorted scaffolds of a draft genome according to a reference genome

Question

[Mehmet]

Dear all,

I would like to sorted scaffolds of a draft genome according to a reference genome. I used Mauve program. It reordered, but when I checked order of scaffolds of the draft genome, it seems that Mauve did not reorder scaffolds of the draft genome.

For instance, in first analysis (alignment of the genomes) scaffold 1 of the reference genome matched with scaffold 116 of the draft. When I reordered, the scaffold 116 did not replaced as the first scaffold of the reference genome.

I am using a worm species genomes for reordering.

[Sej Modha]

Have you tried MCM approach within Mauve? Sorting The Scaffolds After Assembling

[Sej Modha]

Have you tried MCM approach within Mauve? Sorting The Scaffolds After Assembling

[Mehmet]

Yes, I did.

As I mentioned in my question;

"For instance, in first analysis (alignment of the genomes) scaffold 1 of the reference genome matched with scaffold 116 of the draft. When I reordered, the scaffold 116 did not replaced as the first scaffold of the reference genome".

What I want is to change position of scaffolds of the draft genome according to the alignment with the reference genome.

How can I do that?