Apply the tool to virus

[Alice-yyt]

Hello author, i am sorry to disturb you. I want to apply SibeliaZ to virus (for example HIV) to obtain collinear blocks. After that, I will extract SNVs from those collinear blocks. However, I found I can't extract enough SNVs. Do you have some idea to deal with this problem? Thanks a lot!

[iminkin]

Hi,

How do you extract SNV from the blocks?

[Alice-yyt]

Hi,

How do you extract SNV from the blocks?

Thank you for your reply. Yes, I extracted SNVs from blocks.

[iminkin]

Could you please specify more details on how you do that? Do you parse the alignment?

[Alice-yyt]

Could you please specify more details on how you do that? Do you parse the alignment?

Thank you for your reply! Yes, I just parse the alignment and find snvs in every block. After that, I just extract kmer from reference genome which contains the snvs I find in blocks before. (my test is based on the COVID19 database). I am trying to distinguish the subtypes in the COVID19.