jackknifed_beta_diversity.py – A workflow script for performing jackknifed UPGMA clustering and building jackknifed Emperor PCoA plots.

Description:

To directly measure the robustness of individual UPGMA clusters and clusters in PCoA plots, one can perform jackknifing (repeatedly resampling a subset of the available data from each sample).

Usage: jackknifed_beta_diversity.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

The input OTU table in biom format [REQUIRED]

-o, --output_dir

The output directory [REQUIRED]

-e, --seqs_per_sample

Number of sequences to include in each jackknifed subset [REQUIRED]

-m, --mapping_fp

Path to the mapping file [REQUIRED]

[OPTIONAL]

-t, --tree_fp

Path to the tree file [default: None; REQUIRED for phylogenetic measures]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used]

--master_tree

Method for computing master trees in jackknife analysis. “consensus”: consensus of trees from jackknifed otu tables. “full”: tree generated from input (unsubsambled) otu table. [default: consensus]

-f, --force

Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]

-w, --print_only

Print the commands but don’t call them – useful for debugging [default: False]

-a, --parallel

Run in parallel where available [default: False]

-O, --jobs_to_start

Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 1]

Output:

This scripts results in several distance matrices (from beta_diversity.py), several rarefied OTU tables (from multiple_rarefactions_even_depth.py), several UPGMA trees (from upgma_cluster.py), a supporting file and newick tree with support values (from tree_compare.py), and Emperor PCoA plots.

Example:

These steps are performed by the following command: Compute beta diversity distance matrix from otu table (and tree, if applicable); build rarefied OTU tables by evenly sampling to the specified depth (-e); build UPGMA tree from full distance matrix; compute distance matrics for rarefied OTU tables; build UPGMA trees from rarefied OTU table distance matrices; build a consensus tree from the rarefied UPGMA trees; compare rarefied OTU table distance matrix UPGMA trees to either (full or consensus) tree for jackknife support of tree nodes; perform principal coordinates analysis on distance matrices generated from rarefied OTU tables; generate Emperor PCoA plots with jackknifed support.

jackknifed_beta_diversity.py -i otu_table.biom -o bdiv_jk100 -e 100 -m Fasting_Map.txt -t rep_set.tre