Paired-End Amplicon Sequencing was performed on a ~220 bp region in several humanized-mice. I would like to analyze the ASVs and create a table that shows the different variants within the aligned reads to the reference. Most of the available packages that I see are specific to analyzing the microbiome. Are there any packages that would work for non-microbial data? I would like to create an image of the variants similar to the image shown that shows the reference and percentage of variant sequences or some way to get the same data.
I have aligned my reads to the short reference sequence and made some sequence logos but I am unsure of how to analyze the variants, heavily mutated positions and variant seq frequencies.
DADA2 can be used with any kind of amplicon data. Therefore, you can use DADA2 to get the ASV and then align these against the reference sequence