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Old 04-11-2017, 09:33 AM   #3
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Location: California

Join Date: Jul 2014
Posts: 198

I would tend to agree with @thermophile that custom primers would be the way to go here. If you are on a limited budget, Illumina kits tend to be quite expensive on a per-sample basis.

If you are trying to detect co-infections, then yes, simply having tens or hundreds of thousands of reads per sample of any malarial DNA should in theory be sufficient. If you are trying to measure co-infections in a quantitative sense, then I would be more worried about primer bias. Then you could do something like a synthetic control of known lineage amounts, and see how reproducibly you can recover this ground truth using your assay.
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