Using Viral Genomes Other Than HPV16 as Reference (e.g., EBV)

[km-2021]

Can viral genomes other than HPV16, such as EBV, be used as reference genomes?
If so, could you please provide instructions on how to prepare or use them?

[mehrankr]

Yes, you would just need to create the bowtie2 index of any viral genome file of interest.
Please see bowtie2-build documentation.