#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