16S Amplicon Sequencing Workflow

This workflow requires:

• QIIME version 1.9.1 or lower
• SHI7 v.0.9.3 (https://github.com/knights-lab/shi7)
• NINJA v.1.5.1 (https://github.com/GabeAl/NINJA-OPS)
• The dataset provided through Microbiome Helper (https://github.com/LangilleLab/microbiome_helper/wiki/16S-tutorial-(chemerin)
• Basic skills in working from the command line (recommended)

The entire workflow is outlined in the Workflow.md file. You can view it easily in a browser by clicking on it. The workflow includes:

• Quality control of next generation sequencing data with SHI7
• Closed reference OTU picking with NINJA
• Data Exploration with QIIME