Hi, we want to do a MiSeq run of a library pool of TruSeq DNA PCR-free (single index; 6 bp), and custom 16s amplicons (dual index 8+8 bp). We wish the pool to contain 95 % TruSeq library and only 5 % of the amplicons. During the second index read especially, the sequence diversity will be very low if we pool like above. I calculated that the i5 index read will have only ~2 % diversity in every position. Is this enough to obtain good quality in the MiSeq? We could add more of the 16s amplicons to boost the diversity of the index reads. Should I aim for > 5% diversity? Adding more PhiX wouldn't help, since it has no index, right?
Jon
Jon
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