How can I separate amplicon sequences within an Illumina library?

I’m hoping someone can offer some guidance. I have Illumina libraries (one per experimental sample) as fastq files R1/R2 and within each of these is 5 different amplicons (16S, nifH, nosZ etc.). I’d like to separate these out based on the original primers similarly to barcodes but within a library (IE nifH primer vs 16S primer) so I can align them to the functional gene pipeline and repository databases ( I’m not sure how to do this. Is there a better way?

If the primers are still on the sequences then you can name your primers in the oligos file. You could run it with one primer set each time and change the output file name for each primer set.