Workflow of metabarcoding analysis For a diet analysis of an insect-eating animal, all species in a sample shall be identified. For this a sequencing of the metagenomic sample was done, where the COI/COX region was used as a barcode and amplified. This resulted in 20 million reads (after quality control). 

While looking for an apropriate workflow, I am faced with these issues:


For many tools 20 million reads are to much to handle (BLAST for
instance)
For the majority of metagenomic tools the focus is on micro-organisms, not insects
The database to search against must contain COI/COX data, mainly from insects, however, the animal could also eat snails or frog eggs...
Since the reads are amplicons some analysis are not recommended


Leaving me with these questions:


What are the typical analysis steps in a workflow like this?
Which tools could I use for my purpose?
Where could I get a database of COI/COX data?
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.