Identifying Recombination / Translocation Events Across the Reference Genome / Chromosomes

Question

[Toby]

Hi,

I'm trying to map the recombination events / synteny that have occured around my chromosomes of the reference genome, a really good assembly with full length chromosomes. If I dotplot my chromosome / regions of the chromosome I can see some really large scale similarity >100kb in some instances. I've been trying to find a tool that can map these for me, ideally just output the coordinates of similiarity or something I can at least process to that effect.

The tools I've seen seem to either be for populations and detecting against a reference or don't seem to be able to compile, which makes me think I'm missing something.

Thanks,
Toby

[cmdcolin]

are you comparing your genome assembly with a related species to find synteny? or are you looking at self-self alignments? might help get better answers with those details

[Toby]

Self-self alignments between chromosomes to identify shared regions. With these sequences coming from the reference

[cmdcolin]

possibly you could look into calling "segdups" (segmental duplications) in your assembly. that may help with the "translocation" aspect of your interest. I am less familiar with the recombination aspect. maybe having haplotype-specific assemblies would help with that?