Assembly or read mapping which is more appropriate for viral genome sequence data analysis ?

Question

[jeccy.J]

Hi, Biostar community,

We are planning to set up a viral genome analysis pipeline from raw reads to report. Can anyone suggest me some good resource and which protocol should I follow, genome assembly or else I will map the raw reads against some good references and make consensus out of it. What are the pros and cons of both methods?

Best, JC

Answer 1

[coolliuteng]

Maybe you should do both. First, mapping your read to all the virus genome, then the type of the virus can be identified. Second, assemble the reads you have, so that you can get a scanfold.