#Qiime Secondary Analysis

This script creates a batch script for our standard Qiime analysis. It is a very thorough script that runs nearly all possible test. You may need to fine tune some parameters such as the compare_beta iterations

Help:

usage: secondary_analysis.py [-h] -b BIOM -m MAP -p PARAMS -t TRE
                             [-c CATEGORIES] [--qiime17 QIIME17]
                             [--qiime18 QIIME18]

This script runs through a standard QIIME secondary analysis pipeline. The
required input files are the biom, map, tre, and params.

optional arguments:
  -h, --help            show this help message and exit
  -b BIOM, --biom BIOM  The biom file
  -m MAP, --map MAP     The mapping file
  -p PARAMS, --params PARAMS
                        The parameters file
  -t TRE, --tre TRE     The tre file
  -c CATEGORIES, --categories CATEGORIES
                        The metadata categories to compute. Must be colon
                        seperated

Workflow

The pipeline runs the following steps:

• Valadate the parameters file
• Check if Qiime is loaded in the path
• Convert the mapping file to a dictionary
• Summarize biom table
• Summarize taxa through plots
• Compute/Compare Alpha Diversity
• Compute/Compare Beta Diversity
• Compute core microbiome
• Compute OTU category significance (Qiime 1.7)

The Qiime scripts run are:

• source qiime18_path
• print_biom_table_summary.py
• summarize_taxa_through_plots.py
• alpha_rarefaction.py
• compare_alpha_diversity.py
• beta_diversity_through_plots.py
• make_2d_plots.py
• compare_categories.py
• compute_core_microbiome.py
• source qiime17_path
• group_significance.py

Output:

Output is written to the current working directory. A batch file for the Qiime 1.9 commands is created