Workflow of metabarcoding analysis
I'm working on something similar as a side project. I'll detail the steps that I'm using, but I'm curious if others can suggest a better way.


You don't mention if your data are paired-end, but in my case I have paired-end sequences that overlap in the middle. I used FLASh to merge the reads and seqtk to convert the reads to fasta format.
I used the cluster_fast algorithm in vsearch to cluster sequences at 100% identity, then filtered out rare sequence types (&lt;10 sequences) to account for sequencing errors.
This resulted in a manageable number of unique sequences, which I searched against a custom database using vsearch, but which could also have been searched against the nr database using blast.