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MashTree_FASTA

Quick Facts

Workflow Type Applicable Kingdom Last Known Changes Command-line Compatibility Workflow Level
Phylogenetic Construction Bacteria PHB v3.0.0 Yes Set-level

MashTree_FASTA_PHB

MashTree_FASTA creates a phylogenetic tree using Mash distances.

Mash distances are representations of how many kmers two sequences have in common. These distances are generated by transforming all kmers from a sequence into an integer value with hashing and Bloom filters. The hashed kmers are sorted and a "sketch" is created by only using the kmers that appear at the top of the sorted list. These sketches can be compared by counting the number of hashed kmers they have in common. Mashtree uses a neighbor-joining algorithm to cluster these "distances" into phylogenetic trees.

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, etc.) that can be used in Phandango.

Inputs

Terra Task Name Variable Type Description Default Value Terra Status
mashtree_fasta assembly_fasta Array[File] The assembly files for your samples in FASTA format Required
mashtree_fasta cluster_name String Free text string used to label output files Required
mashtree_fasta 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
mashtree_fasta 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
mashtree_fasta data_summary_terra_table String The name of the sample-level Terra data table that will be used for generating a data summary Optional
mashtree_fasta 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
mashtree_fasta midpoint_root_tree Boolean If true, midpoint root the final tree FALSE Optional
mashtree_fasta 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
mashtree_fasta sample_names Array[String] The list of samples Optional
mashtree_task cpu Int Number of CPUs to allocate to the task 16 Optional
mashtree_task disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional
mashtree_task docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/mashtree:1.2.0 Optional
mashtree_task genomesize Int Genome size of the input samples 5000000 Optional
mashtree_task kmerlength Int Hashes will be based on strings of this many nucleotides 21 Optional
mashtree_task memory Int Amount of memory/RAM (in GB) to allocate to the task 64 Optional
mashtree_task mindepth Int If set to zero, mashtree will run in "accurate" mode as it will chose a mindepth by itself in a slower method; this value otherwise indicates the minimum number of times a kmer must appear in order to be included 5 Optional
mashtree_task sketchsize Int Each sketch will have at most this many non-redundant min-hashes 10000 Optional
mashtree_task sort_order String For neighbor-joining, the sort order can make a difference. Options include: "ABC" (alphabetical), "random", "input-order" ABC Optional
mashtree_task truncLength Int How many characters to keep in a filename 250 Optional
reorder_matrix cpu Int Number of CPUs to allocate to the task 100 Optional
reorder_matrix disk_size Int Amount of storage (in GB) to allocate to the task 2 Optional
reorder_matrix docker String The Docker container to use for the task 100 Optional
reorder_matrix 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 1 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

MashTree_FASTA Details

MashTree_FASTA is run on a set of assembly fastas and creates a phylogenetic tree and matrix.

MashTree_FASTA Technical Details

Links
Task task_mashtree_fasta.wdl
Software Source Code Mashtree on GitHub
Software Documentation Mashtree on GitHub
Original Publication(s) Mashtree: a rapid comparison of whole genome sequence files
Data summary (optional)

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 does not add a Phandango coloring tag to group items from the same column, but you can turn this on by setting phandango_coloring to true.

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

Data summary technical details

Links
Task task_summarize_data.wdl

Outputs

Variable Type Description
mashtree_docker String The Docker image used to run the mashtree task
mashtree_filtered_metadata File Optional output file with filtered metadata that is only produced if the optional summarize_data task is used
mashtree_matrix File The distance matrix made
mashtree_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
mashtree_tree File The phylogenetic tree made
mashtree_version String The version of mashtree used in the workflow
mashtree_wf_analysis_date String The date the workflow was run
mashtree_wf_version String The version of PHB the workflow is hosted in

References

Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762, https://doi.org/10.21105/joss.01762

Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016). Mash: Fast genome and metagenome distance estimation using minhash. Genome Biology, 17(1), 132. doi:10.1186/s13059-016-0997-x