I am looking to find a way to locate centromeres in a genome assembly.
Any recommendations ?
Thanks for your help.
Is it something well-annotated like human/mouse/fly/worm or a complete de novo assembly?
it's a complete de novo assembly of non model organism.
I don't expect your assembly actually includes the centromere. Did you use long reads? How many scaffolds do you have and how many chromosomes do you expect?
Yes it's a PacBio assembly at contig level (around 10k contigs).
My species has 12 pairs of chromosomes.
Then chances are that your contigs are broken at the centromeres and do not span those.
could you give more explanation please ?
Centromeres are long and repetitive. Assembly across long and repetitive sequences is hard.
Also not easily sequenceable with current technologies we have. See this.
What have you tried so far?
A quick google search brings up a couple of articles that seem to address the assembly of centromeres in different species: Drosophila, Grey Mouse Lemur, Human, Bovidae
Thanks for the papers ! , I will take a look.