Question

Assembly or alignment?

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21 months ago

deniselavezzari • 0

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.

sequencing reads assembly alignment • 584 views

ADD COMMENT • link updated 21 months ago by colindaven 6.4k • written 21 months ago by deniselavezzari • 0

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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.

ADD REPLY • link 21 months ago by GenoMax 141k

score 2 · Answer 1 · 2022-07-20

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...