I have been trying out different programs to analyze amplicons sequenced by an Illumina MiSeq. Originally I gave AmpliSAS a try, and the program seems to eliminate too many MHC alleles from each individual, and only allows uploads of 500mb files.
I thought mothur may be a good program to cluster my reads, do quality control, and assign my alleles as OTUs, which wouldn't be a problem, but I ran into trouble with that too as their SOP is designed for microbiome data, and I just can't get it to work for my data.
So, does anyone know of any program that would work with amplicons by merging paired-end files, trim the oligos (barcodes were trimmed by my genomics center already), do a quality control check, and then assign the amplicons to each individual?
Any help is greatly appreciated!