Protein abundance-Metagenomes

Question

[erinda]

I would greatly appreciate your assistance with a task I am currently working on. I have approximately 300 metagenomes and am trying to quantify the abundance of specific proteins (using the raw reads from the metagenomes). Could a DIAMOND-based approach be effective in this case? I am new to this field, so any guidance would be helpful.

[GenoMax]

Are you planning to search with DIAMOND against a set of specific proteins or something more generic like swissprot/nr? Depending on the protein you are looking at (and the domains etc that may be shared with other unrelated proteins) the results you get may need to be carefully parsed. But in terms of getting the job done quicker than blast+, this should work. Provided you have the necessary hardware.