Assembly or alignment?
Hi!
I have a dilemma. I have a virus that I don't know how similar it is to the reference one. I want to understand if it is better to try to assembly or to align to the reference and create a consensus. Which are the pro and cons? Thanks a lot.
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colindaven
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deniselavezzari •
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deniselavezzari •
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I would start by taking as many viral strains as you can find as a reference. Align reads against these, then call SNPs. This should give you a very good picture.
Assembly is hard with viruses, since they are co-cultured with eg mouse or human cells, and these make up the bulk of the reads in a read dataset.
But then - this all depends on your data, and you didn't mention that at all...
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Try both options. Viruses are (relatively) small so you are not going to spend inordinate amount of time on these analyses.