I never used Qiime2 before and I was trying to understand how I can demultiplex my reads.
I have two fasq.gz file of paired-end reads from Illumina Miseq 2x150 sequencing. My reads have a sample 8 bases sample tag and 2/4 leading Ns. Both forward and reverse primers are tagged, so I used a combinatorial indexing approach. I can create a tsv with each sample-tag combination.
I have found various q/a regarding this topic so I am so sorry if this post is redundant but I can not figure out which plugin or external tool I can use.
(I work on freshwater eDNA, I have amplyfied the 12s for fishes and CO1 for invertebrates so I have already analyzed my reads using Obitools retriving the MOTUs, now I want to retrives the ASVs)