genomeDistance

Options

Option	Description	Argument
--samples	Sample names. It determines the plotting order If “NA” all samples are used [default NA]	[char …]
--gipOut	GIP output director [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/genomeDistance]	[char]
--contextGenomes	Two columns TSV file listing additional genomes. Syntax: name<Tab>filePath [default NA]	[char]
--customColors	TSV file with 2 columns named “SAMPLE” and “COLOR” indicating the color to be used for each sample. If “NA” all samples are shown in black [default NA]	[char]
--phylogenyDistance	Distance matrix e.g. the phylogeny.treefile.distMat.gz file produced with the phylogeny module. If “NA” the ANI distance is measured [dafault NA]	[char]
--PCAlabel	Show PCA labels [default all]	[all|none]
--debug	Dump session and quit
-h, --help	Show help message

Description

The genomeDistance module is meant to compare the genomic distance of the samples of interest.

For each sample the module loads the genome file embedding the predicted filtered SNVs (pseudoReference.fa.gz files), then measures the ANI (average nucleotide identity) scores between all sample pairs. The resulting distance is then used to run a principal component analysis (PCA) and produce a dendrogram plot demonstrating the measured distances.

Alternatively this module can be use to generate distance plots of a custom input matrix generated with the phylogeny module.

Example

From the GIP worked example folder execute

giptools genomeDistance

This will generate the two genomeDistance output files in the gipOut/sampleComparison folder.

The genomeDistance.pdf file include dendrogram and PCA plot representations of the genomic distances between samples. For example, the dendrogram and the PCA graph of variables generated in this example are the following:

The genomeDistance.xlsx file reports the computed ANI scores for all sample pairs.