Hello,

I decided to use the Dada2 basic pipeline for 16S in order to detect variants in my viral amplicon sequences. I have PCR amplified sequences from a 302 base-pair region of the viral genome. I used the DADA2 pipeline to detect the variants because I like chart with counts for each ASV that it outputs at the end. We have variants for 6 different time-points to track if there is a tropism switch between which virus predominates over time. I of course just skip the phylogeny step. Is there any bias towards microbiome sequencing in the pipeline that I used?

At a late time-point, a clear tropism switch is evident but the asv that is most dominate matches the reference exactly and if this had evolved from a tropism switch to this virus type then it wouldn't likely match exactly. Perhaps it is contamination. I am wondering if there is any aspect of the dada() function that would not be appropriate for finding the variants of my viral sequences?

Thanks, SARA