What Does a Typical 16S Run Look Like on a MiSeq?
A typical 16S run on the MiSeq has the %Base and Q30 patterns shown below (in a 2x300 bp run). %Base
The drop in the quality in the first cycles is due to the insert beginning with the sequencing of a locus specific primer.
Due to the low diversity of these libraries, the recommended cluster density for a 16S run is 30-40% lower than the standard density guidelines on the MiSeq.
For more information regarding low-diversity sequencing, review Illumina's Cluster Optimization Overview Guide and the Illumina Knowledge article How much PhiX spike-in is recommended when sequencing low diversity libraries on Illumina platforms?
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