Closed:DNA Sequencing of Single Genome Amplicons analysis

Question

[pennakiza]

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!