Skip to content

kSNP3

Quick Facts

Workflow Type Applicable Kingdom Last Known Changes Command-line Compatibility Workflow Level
Phylogenetic Construction Bacteria, Mycotics, Viral PHB v2.1.0 Yes; some optional features incompatible Set-level

kSNP3_PHB

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.

You can learn more about the kSNP3 workflow, including how to visualize the outputs with MicrobeTrace in the following video: 📺 Using KSNP3 in Terra and Visualizing Bacterial Genomic Networks in MicrobeTrace

Inputs

Terra Task Name Variable Type Description Default Value Terra Status
ksnp3_workflow assembly_fasta Array[File] The assembly files to be analyzed Required
ksnp3_workflow cluster_name String Free text string used to label output files Required
ksnp3_workflow samplename Array[String] The set of sample names Required
core_ksnp3_shared_snps_task disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
core_reorder_matrix cpu Int Number of CPUs to allocate to the task 2 Optional
core_reorder_matrix disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
core_reorder_matrix docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Optional
core_reorder_matrix memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
core_snp_dists cpu Int Number of CPUs to allocate to the task 1 Optional
core_snp_dists disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
core_snp_dists docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Optional
core_snp_dists memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
ksnp3_task cpu Int Number of CPUs to allocate to the task 4 Optional
ksnp3_task disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
ksnp3_task docker_image String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/ksnp3:3.1 Optional
ksnp3_task kmer_size Int The length of kmer containing the SNP you want kSNP3 to use 19 Optional
ksnp3_task ksnp3_args String Additional arguments you want kSNP3 to use; e.g., "-ML" or "-NJ" Optional
ksnp3_task memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
ksnp3_task previous_ksnp3_snps File File with existing SNPs for the current run to be appended to. Optional
ksnp3_workflow data_summary_column_names String A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes" Optional
ksnp3_workflow data_summary_terra_project String The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL Optional
ksnp3_workflow data_summary_terra_table String The name of the sample-level Terra data table that will be used for generating a data summary Optional
ksnp3_workflow data_summary_terra_workspace String The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project. Optional
ksnp3_workflow midpoint_root_tree Boolean If true, midpoint root the final tree FALSE Optional
ksnp3_workflow phandango_coloring Boolean Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true. FALSE Optional
pan_reorder_matrix cpu Int Number of CPUs to allocate to the task 100 Optional
pan_reorder_matrix disk_size Int Amount of storage (in GB) to allocate to the task 2 Optional
pan_reorder_matrix docker String The Docker container to use for the task 100 Optional
pan_reorder_matrix memory Int Amount of memory/RAM (in GB) to allocate to the task us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Optional
pan_snp_dists cpu Int Number of CPUs to allocate to the task 1 Optional
pan_snp_dists disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional
pan_snp_dists docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Optional
pan_snp_dists memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional
summarize_data cpu Int Number of CPUs to allocate to the task 8 Optional
summarize_data disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
summarize_data docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Optional
summarize_data id_column_name String If the sample IDs are in a different column to samplenames, it can be passed here and it will be used instead. Optional
summarize_data memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional
version_capture docker String The Docker container to use for the task "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" Optional
version_capture timezone String Set the time zone to get an accurate date of analysis (uses UTC by default) Optional

Workflow 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.

If you fill out the data_summary_* and sample_names optional variables, you can use the optional summarize_data task. The task takes a comma-separated list of column names from the Terra data table, which should each contain a list of comma-separated items. For example, "amrfinderplus_virulence_genes,amrfinderplus_stress_genes" (with quotes, comma separated, no spaces) for these output columns from running TheiaProk. The task checks whether those comma-separated items are present in each row of the data table (sample), then creates a CSV file of these results. The CSV file indicates presence (TRUE) or absence (empty) for each item. By default, the task adds a Phandango coloring tag to group items from the same column, but you can turn this off by setting phandango_coloring to false.

Example output CSV 
1
2
3
4
Sample_Name,aph(3')-IIa,blaCTX-M-65,blaOXA-193,tet(O)
sample1,TRUE,,TRUE,TRUE
sample2,,,FALSE,TRUE
sample3,,,FALSE,
Example use of Phandango coloring

Data summary produced using the phandango_coloring option, visualized alongside Newick tree at http://jameshadfield.github.io/phandango/#/main

Example phandango_coloring output

Phandango coloring example

Outputs

Variable Type Description
ksnp3_core_snp_matrix File The SNP matrix made with the core genome; formatted for Phandango if phandango_coloring input is true
ksnp3_core_snp_matrix_status String Will print either The core SNP matrix was produced OR The core SNP matrix could not be produced
ksnp3_core_snp_table File Formatted version of ksnp3_vcf_ref_genome file with only core SNPs, sorted by number of occurrences in the sample set
ksnp3_core_tree File The phylogenetic tree made with the core genome
ksnp3_docker String The docker image used
ksnp3_filtered_metadata File Optional output file with filtered metadata that is only produced if the optional summarize_data task is used.
ksnp3_ml_tree File Maximum likelihood tree that is only produced if ksnp3_args includes "-ML"
ksnp3_nj_tree File Neighbor joining tree that is only produced if ksnp3_args includes "-NJ"
ksnp3_number_core_snps String Number of core SNPs in the sample set
ksnp3_number_snps String Number of SNPs in the sample set
ksnp3_pan_snp_matrix File The SNP matrix made with the pangenome; formatted for Phandango if phandango_coloring input is true
ksnp3_pan_tree File The phylogenetic tree made with the pangenome
ksnp3_snp_dists_version String The version of snp_dists used in the workflow
ksnp3_snps File File containing the set of SNPs used in the analysis. Required if more trees are to be appended to the existing one.
ksnp3_summarized_data File CSV presence/absence matrix generated by the summarize_data task from the list of columns provided; formatted for Phandango if phandango_coloring input is true
ksnp3_vcf_ref_genome File A VCF file containing the variants detected in the core genome
ksnp3_vcf_ref_samplename String The name of the (user-supplied) sample used as the reference for calling SNPs.
ksnp3_vcf_snps_not_in_ref File A TSV file of the SNPs not present in the reference genome, but were identified by kSNP3.
ksnp3_wf_analysis_date String The date the workflow was run
ksnp3_wf_version String The version of the repository the workflow is hosted in

References

Shea N Gardner, Tom Slezak, Barry G. Hall, kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome, Bioinformatics, Volume 31, Issue 17, 1 September 2015, Pages 2877–2878, https://doi.org/10.1093/bioinformatics/btv271

https://github.com/tseemann/snp-dists