Platinum Hot Start versus Q5 Hot Start Hifi PCR kits

Dear EMP protocol users - I have been using EMP's 18S protocol to sequence eDNA from marine sediments. Before ordering the expensive 18S ultra primers, we ordered just the gene specific primers for testing purposes. I run PCR with two kits using these 1391F and EukBr non-barcoded primers- [Invitrogen's Platinum Hot Start 2x master mix](https://www.thermofisher.com/order/catalog/product/13000012) and [NEB's Q5 Hot Start Hifi 2x master mix](https://www.neb.com/products/m0494-q5-hot-start-high-fidelity-2x-master-mix#Product%20Information).

I got much stronger bands with Q5 than Platinum Hot Start (see gel image). [NEB claims that Q5 has much better fidelity](https://www.neb.com/products/pcr-qpcr-and-amplification-technologies/q5-high-fidelity-dna-polymerases/q5-high-fidelity-dna-polymerases) compared to Platinum Hot Start.

So I'm thinking about switching PCR kits but wanted to check if anyone else has tried a different PCR kit with EMP protocols regarding of the gene? I would like to stick to EMP's protocol if possible but I also have concerns about their recommended PCR kit.

Any suggestions or thoughts are appreciated. Thank you! -Taruna

No source file, test, or entry point is identified; start by reviewing the 18S protocol context and the reported comparison between Platinum Hot Start and Q5 Hot Start HiFi PCR kits. The issue does not define a documentation change or a concrete completion criterion, so the expected deliverable would need clarification first.

Written by the indexing model from the issue text.