How does the 16S-SNAPP data analysis pipeline work?

The 16S-SNAPP tool is designed to generate sequence features and taxonomic assignments of them by associating reads from different amplicon regions. 

It does this in two steps:
1. It uses a reference-based approach to associate reads from different V-region amplicons to their highest identity, closest references (assumed templates), and generates consensus sequences, which are made up of amplicon reads mapped to the same templates. This process works well for recovering longer, near full-length 16S V-region sequences (depending on sequencing depth and quality), from the multi-V-region amplicon pool created by the xGen 16S Amplicon Panel v2.

2. It classifies the consensus sequences. This is currently carried out using RDP Classifier at genus level resolution. We are currently improving this process towards species-level resolution.