jackknifed_beta_diversity.py – A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D 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 fasta file [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 rarified otu tables (from multiple_rarefactions.py) several UPGMA trees (from upgma_cluster.py), a supporting file and newick tree with support values (from tree_compare.py), and 2D and 3D PCoA plots.

Example:

These steps are performed by the following command:

1. Compute beta diversity distance matrix from otu table (and tree, if applicable)
2. Build rarefied OTU tables;
3. Build UPGMA tree from full distance matrix;
4. Compute distance matrics for rarefied OTU tables;
5. Build UPGMA trees from rarefied OTU table distance matrices;

5.5 Build a consensus tree from the rarefied UPGMA trees

6. Compare rarefied OTU table distance matrix UPGMA trees to either (full or consensus) tree for jackknife support of tree nodes.
7. Perform principal coordinates analysis on distance matrices generated from rarefied OTU tables.
8. Generate 2D and 3D PCoA plots with jackknifed support.

jackknifed_beta_diversity.py -i inseqs1_otu_table.txt -t inseqs1_rep_set.tre -p custom_parameters_jack.txt -o wf_jack -e 5 -v -m mapping_file.txt