Question: Assembly or read mapping which is more appropriate for viral genome sequence data analysis ?
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gravatar for jeccy.J
9 months ago by
jeccy.J50
Argentina
jeccy.J50 wrote:

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

read mapping assembly • 199 views
ADD COMMENTlink modified 9 months ago by coolliuteng10 • written 9 months ago by jeccy.J50
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gravatar for coolliuteng
9 months ago by
coolliuteng10
coolliuteng10 wrote:

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.

ADD COMMENTlink written 9 months ago by coolliuteng10
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