Overview

The kSNP3 workflow is for phylogenetic analysis of bacterial genomes using single nucleotide polymorphisms (SNPs). The kSNP3 workflow identifies SNPs amongst a set of genome assemblies, then calculates a number of phylogenetic trees based on those SNPs:

Pan-genome phylogenetic trees: The term “pan-genome” is used here to describe the collective genetic content amongst the set of genomes, including regions outside of genes and other coding sequences. Outputs based on the pan-genome are labeled with _pan.
Core-genome phylogenetic trees: The kSNP3 workflow will also generate phylogenetic trees based on the core genome (genetic content that is present in all members of the set of genomes). Outputs based on the core-genome are labeled with _core.

This workflow also features an optional module, summarize_data that creates a presence/absence matrix for the analyzed samples from a list of indicated columns (such as AMR genes, plasmid types etc.). If the phandango_coloring variable is set to true, this will be formatted for visualization in Phandango, else it can be viewed in Excel.

Inputs

Required User Inputs

Optional User Inputs

Tasks/Actions

The ksnp3 workflow is run on the set of assembly files to produce both pan-genome and core-genome phylogenies. This also results in alignment files which - are used by snp-dists to produce a pairwise SNP distance matrix for both the pan-genome and core-genomes.

The optional summarize_data task performs the following only if all of the data_summary_* and sample_names optional variables are filled out:

Digests a comma-separated list of column names, such as "amrfinderplus_virulence_genes,amrfinderplus_stress_genes", etc. that can be found within the origin Terra data table.
It will then parse through those column contents and extract each value; for example, if the amrfinder_amr_genes column for a sample contains these values: "aph(3')-IIIa,tet(O),blaOXA-193", the summarize_data task will check each sample in the set to see if they also have those AMR genes detected.
Outputs a .csv file that indicates presence (TRUE) or absence (empty) for each item in those columns; that is, it will check each sample in the set against the detected items in each column to see if that value was also detected.

By default, this task appends a Phandango coloring tag to color all items from the same column the same; this can be turned off by setting the optional phandango_coloring variable to false.

Outputs

All outputs

References

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