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DNA Sequencing of Single Genome Amplicons analysis
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14 months ago
pennakiza • 20

Hello all,

I have a few DNA sequencing reads (Illumina) for HIV amplicons that are supposed to derive from single genome amplification. I have picked the samples based on the band size when run on my gel and now I'd like to confirm that my sequences are indeed coming from a single genome and that they are the gene that are supposed to be. Which way do you think should be the best?

Thank you!

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How many sequences/amplicons are there? One option is to align to a reference and call SNP.

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I have 96 amplicons - I consider each one of them a different sample although they come from the same patient. I'm just a bit worried about SNP calling, as it's HIV Env and I am not sure how accurate would that be, considering the high variance in different quasi species? I'm sorry if I sound silly, I have just started working with DNA seq and HIV!

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