Request for Custom Scripts: Rearrangement Breakpoints filtering and Interchromosomal Rearrangement Identification

[Caoyu819]

Dear AGORA team,

I'm currently working on genome structure evolution in the Fagales order. Your AGORA pipeline has been incredibly helpful, aiding me in reconstructing ancestral genomes. Thanks for this fantastic tools.

Now I'm keen on studying rearrangement breakpoints and their correlation with phenotypic innovation. While I understand the process to computing rearrangement breakpoints from the AGORA paper's Supplementary Information ('Vertebrate genome evolutionary dynamics'), I'm struggling with practical implementation.

I've looked extensively on AGORA's GitHub but haven't found the relevant custom Python/Perl scripts. Could you kindly share these scripts for rearrangement breakpoints filtering and interchromosal rearrangement identification? They would greatly assist my ancestral genome reconstruction analysis.

Thank you very much in advance. looking forward to cite your paper and pipeline soon.

With best wishes,
Yu