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?