Dear experts,
I am planning to generate a large numbers of Illumina libraries in an ongoing project. These will be amplified via a single PCR step, in which the indexed adapters are added to the PCR primers. Can I just order such primers as normal PCR primers including the indices or will their quality be insufficient for NGS application (regarding index hopping etc.)? The commercially available kits for indexing are very expensive.
I would be very grateful if anyone who did this already could share some experiences. Kind regards and thank you in advance, Matthias
PS:
In case more information is required, this is the PCR protocol which I am trying to run:
https://media.addgene.org/cms/filer_public/61/7b/617bc56c-e53e-42f8-a7c9-3c28b429aced/n16_amplification_1.pdf
Sure, as long as you know what you are doing, you can synthesize/order you own primers - I would check it with your sequencing guy though, Illumina primers/probes change pretty often and you want to make sure you have all the modifications. With that said, I would advise against it though, it is waaay easier and cheaper to let your sequencing center prep your libraries, and that way you have a better chance to get the results you want.
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