Entering edit mode
9.5 years ago
Gon
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10
Hi! I want to detect possible drug-resistance mutations in HIV minority variants. I'm working with a Illumina library, and I've managed to get .sam files with the reads aligned to a reference sequence, but I'm stuck on what to do next. I don't want to create a consensus of the reads, but instead, explore the amino acid diversity across the reads in certain positions related to drug-resistance. So, I was wondering if anyone had any suggestion regarding programs/pipelines (ideally free) that could help me do that.
Thank you!
Thanks Jeremy, I know Stanford's tool but I'm afraid in doesn't work for NGS data. What I'm looking for is resistance mutations in minority variants within a patient, and I have >50,000 Illumina reads that would crash the HIVdb... But thanks anyway!
That's not too many for the web service (as opposed to the web site). I did 100k reads over 7 years ago: http://nar.oxfordjournals.org/content/35/13/e91.long
Oh, that's quite different, then! In that case, it's worth trying (I already applied for a user key). I didn't understand you the first time, sorry. Thanks for the info!