Does anyone know how to get a consensus genome from NGS data indicating the 
percent variance at each nucleotide? I have a small virus genome with manyfold 
coverage from my transcriptomic run. I'd like to know what the transcriptome 
indicates is the actual genome plus get a feel for any hotspots where there 
appears to be significant varience from the reference sequence (i.e. because 
the reference is wrong or perhaps because of frequent errors in that region due 
to RNA pol II having a problem accurately transcribing the sequence).

Many thanks!


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