Customized reference genome (virus genome added)

Question

[kimmitzka]

Hi all,

Recently I have read some paper related to SARS-Cov-2. For some RNA-seq analysis, there was usually saying that the human reference genome also with a SARS-Cov-2 virus genome added. I really wonder that why they added the virus genome. And I would really appreciate if someone can tell me how to add a customized referece genome.

Thanks very much!! kimi