Subcommand: squash - lczech/gappa GitHub Wiki

Perform Squash Clustering for a set of samples.

Usage: gappa analyze squash [options]

Input
--jplace-path	Required. TEXT:PATH(existing)=[] ... List of jplace files or directories to process. For directories, only files with the extension .jplace[.gz] are processed.
Settings
--exponent	FLOAT=1 Exponent for KR integration.
--point-mass	FLAG Treat every pquery as a point mass concentrated on the highest-weight placement. In other words, ignore all but the most likely placement location (the one with the highest LWR), and set its LWR to 1.0.
--ignore-multiplicities	FLAG Set the multiplicity of each pquery to 1.0. For phylogenetic placement, the multiplicity is the equivalent of read abundances. This flag hence ignores the read abundances, treating each pquery as a singleton.
Color
--color-list	TEXT=BuPuBk List of colors to use for the palette. Can either be the name of a color list, a file containing one color per line, or an actual comma-separated list of colors. Colors can be specified in the format #rrggbb using hex values, or by web color names.
--reverse-color-list	FLAG If set, the order of colors of the --color-list is reversed.
--log-scaling	FLAG If set, the sequential color list is logarithmically scaled instead of linearily.
Output
--out-dir	TEXT=. Directory to write output files to.
--file-prefix	TEXT File prefix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--file-suffix	TEXT File suffix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
Tree Output
--write-newick-tree	FLAG If set, the tree is written to a Newick file. This format cannot store color information.
--write-nexus-tree	FLAG If set, the tree is written to a Nexus file. This can for example be opened in FigTree.
--write-phyloxml-tree	FLAG If set, the tree is written to a Phyloxml file. This can for example be used in Archaeopteryx.
--write-svg-tree	FLAG If set, the tree is written to a SVG file. This gives a file for vector graphics editors.
Newick Tree Output
--newick-tree-branch-length-precision	INT=6 Needs: --write-newick-tree Number of digits to print for branch lengths in Newick format.
--newick-tree-quote-invalid-chars	FLAG Needs: --write-newick-tree If set, node labels that contain characters that are invalid in the Newick format (i.e., spaces and :;()[],{}) are put into quotation marks. If not set (default), these characters are instead replaced by underscores, which changes the names, but works better with most downstream tools.
Svg Tree Output
--svg-tree-shape	TEXT:{circular,rectangular}=circular Needs: --write-svg-tree Shape of the tree.
--svg-tree-type	TEXT:{cladogram,phylogram}=cladogram Needs: --write-svg-tree Type of the tree, either using branch lengths (phylogram), or not (cladogram).
--svg-tree-stroke-width	FLOAT=5 Needs: --write-svg-tree Svg stroke width for the branches of the tree.
--svg-tree-ladderize	FLAG Needs: --write-svg-tree If set, the tree is ladderized.
Global Options
--allow-file-overwriting	FLAG Allow to overwrite existing output files instead of aborting the command.
--verbose	FLAG Produce more verbose output.
--threads	UINT Number of threads to use for calculations.
--log-file	TEXT Write all output to a log file, in addition to standard output to the terminal.

Performs Squash Clustering. The command is a re-implementation of guppy squash, see there for more details.

The main output of the command is a cluster hierarchy tree that shows which input jplace samples are clustered close to each other. Although the tree is written to Newick format, it is not a phylogeny, as its tips represent samples (jplace files). The inner node labels are numbered consecutively starting at n, with n being the number of samples used as input.

If the --write-...-tree options are used, the mass trees representing the samples (tips of the cluster tree) and the mass trees of the inner nodes (average masses of the corresponding tips) are written for visualization. Their numbering is 0 to n-1 for the tips (samples), and n to 2n-2 for the inner nodes (cluster averages). These trees can help to explore how and why the samples were clustered during the algorithm.

When using this method, please do not forget to cite

Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa070

Frederick Matsen, Steven Evans. Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison. PLOS ONE, 2013. doi:10.1371/journal.pone.0056859