Question: Sorted scaffolds of a draft genome according to a reference genome
1
gravatar for Mehmet
3.2 years ago by
Mehmet660
Japan
Mehmet660 wrote:

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.

ADD COMMENTlink written 3.2 years ago by Mehmet660
1

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

ADD REPLYlink written 3.2 years ago by Sej Modha4.7k

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

ADD REPLYlink written 3.2 years ago by Sej Modha4.7k

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?

ADD REPLYlink written 3.2 years ago by Mehmet660
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