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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 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: 2]

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: 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 2D and 3D 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

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