Core Diversity Analysis

http://qiime.org/scripts/core_diversity_analysis.html

Description

After covering alpha-diversity, beta-diversity and composition analysis scripts, we can introduce the master of all workflows, core_diversity_analysis.py. This workflow performs all the steps we have just followed above. It does alpha, beta, taxonomy, significance and a few others. Most of the analysis this workflow does by default will not help answer specific questions. It is more of a way to analyze your data at a glace by running every command at once. You can make this command more powerful by adding a parameters file and customizing each step.

One way to use this script is to customize the alpha diversity parameter and add all the alpha diversity metrics and it will run statistics on all of them. And you can add multiple groups so it will compare multiple column varibles. It is recommended to use individual analysis scripts to avoid any unwanted rarefactions (which is performed by default during the first step!).

Parameters

--input_biom_fp | -i
Input OTU table in .biom format

--output_dir | -o
The name and location of the output folder

--mapping_fp | -m
The mapping file that corresponds to the input OTU table

--categories | -c
The categories to perform analyses on. Multiple categories must be separated by commas. e.g Treatment,Timepoint,Sex

--tree_fp | -t
Phylogenetic Tree file (.tre)

--sampling_depth | -e
An even sampling depth to rarefy your OTU table. This rareified table will be used in all downstream analyses.

--recover_from_failure
an option to keep the command running if it encounters an folder.

Command

 core_diversity_analyses.py \
 -i otu_table.biom \
 -o core_output \
 -m mapping_file.txt \
 -c SampleType,Year \
 -t rep_set.tre \
 -e 1000 \
 --recover_from_failure

Output

The command will generate many files, so it also creates a .html file which organizes the data