A meta script to take care of the Qiime secondary analysis
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#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


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


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:


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