These pages include exercises from workshops I have taught at Michigan State University. They cover the use of RDP’s web-based and command line tools for processing and classifying:
- 16S rRNA gene sequences from Bacteria and Archaea
- 28S rRNA gene sequences from Fungi
- ITS2 sequences from Fungi
- Functional gene sequences
Xander is a targeted functional gene assembler, but the pipeline presented here includes steps for further processing all the way to creating an experiment level phyloseq object containing an OTU table, taxonomy table, representative sequences and sample data table.