Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform
To assign an Illumina read to a particular sample, one examines both of the barcodes at each end of the sequence. In green, the two barcodes agree on which sample the read is coming from. In black, no barcodes are found on either end. In yellow, only one barcode is present. In orange, the two barcodes come from the same directional set and should not be found together (e.g. two forward barcodes). In red, the two barcodes each indicate a different sample. Overall, with this setup, about half of the raw data is discarded.