Has anyone ever tried doing an amplicon sequencing on "non-enriched" amplicons? The idea is to basically just fragment everything, add Truseq adapters (with indexes) and then sequence using a custom sequencing primer and index 1 primer?
I do realize that getting such samples to satisfying cluster densities (of sequenceable fragments) might be very hard due to the presence of undesired fragments which would also form clusters. But what if you could reduce the overall noise of undesired fragments (but not eliminate them completely), would this direct sequencing then have more sense?
I would just like to get completely rid of the PCR bias before sequencing...
Any thoughts?
I do realize that getting such samples to satisfying cluster densities (of sequenceable fragments) might be very hard due to the presence of undesired fragments which would also form clusters. But what if you could reduce the overall noise of undesired fragments (but not eliminate them completely), would this direct sequencing then have more sense?
I would just like to get completely rid of the PCR bias before sequencing...
Any thoughts?
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