Pipeline for 16S rRNA processing using DADA2

Here you will find all of the code and explanations to completely reproduce our DADA2 pipeline for processing raw, pair-end 16S rRNA Illumina amplicon data. <br> The pipeline consists of two (2) parts of the workflow. <br> 1. The first part will process the data from different runs separately. Samples were sequenced across three runs, each of which was processed separately. This part consists of steps to filter and trim, learn errors, dereplicate, infer amplicon sequence variants (ASV), and merge paired end reads. We also include an optional step for identifying chimeras and assigning taxonomy for each run individually, however we actually did this on the combined data set in the next part. <br> 2. In the second part we merge the outputs from the first part, identify chimeras, and assign taxonomy. <br> Also included is the HTML file for the workflow. This can be viewed in any web browser.<br>