About the selection of reference genome

[cnxiaobo94]

Hi, dear friends. I have a question on processing rawdata. When I made PCA or Dst. analyses, I need to take a outgroup species as reference genome for processing rawdata. My question is that whether the existing genomes of the analyzed species can be used as reference genomes to processing sequence data for PSMC analysis?

[plubbe]

Depends on how taxonomically distant the reference is from your data. You may find this paper helpful from Prasad et al, 2021