Usher¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Phylogenetic Placement | Viral | PHB v2.1.0 | Yes | Sample-level, set-level |
Usher_PHB¶
UShER (Ultrafast Sample Placement on Existing Trees) rapidly places new samples onto an existing phylogeny using maximum parsimony. This workflow uses the UCSC-maintained global trees for SARS-CoV-2, mpox, RSV-A, and RSV-B if those organisms are specified in the organism input field. However, UShER can be used on any organism as long as a mutation-annotated tree (MAT) is provided in protobuf format. Contact us if you need help generating your own mutation-annotated tree, or follow the instructions available on the UShER wiki here.
Inputs¶
While this workflow is technically a set-level workflow, it works on the sample-level too. When run on the set-level, the samples are placed with respect to each other.
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status | | |---|---|---|---|---|---| | usher_workflow | assembly_fasta | Array[File] | The assembly files for the samples you want to place on the pre-existing; can either be a set of samples, an individual sample, or multiple individual samples | | Required | | usher_workflow | organism | String | What organism to run UShER on; the following organism have default global phylogenies and reference files provided: sars-cov-2, mpox, RSV-A, RSV-B. | | Required | | usher_workflow | tree_name | String | The output prefix for the uncondensed tree output and the clades output. | | Required | | usher | cpu | Int | Number of CPUs to allocate to the task | 8 | Optional | | usher | disk_size | Int | Amount of storage (in GB) to allocate to the task | 200 | Optional | | usher | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/pathogengenomics/usher:0.6.2 | Optional | | usher | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 32 | Optional | | usher | mutation_annotated_tree_pb | File | Required for organisms other than sars-cov-2, mpox, RSV-A or RSV-B. This is the mutation-annotated global phylogeny upon which your samples will be placed | | Optional, Required | | usher | reference_genome | File | Required for organisms other than sars-cov-2, mpox, RSV-A or RSV-B. This is the reference genome used to determine your sequence's mutations to accurately place the sample on the phylogeny. | | Optional, Required | | usher | subtree_size | Int | Indicates how many of the closest-related samples you want to show in a subtree; more subtrees are made if there is more sequence diversity in the set of input samples (multiple subtrees are only generated if this workflow is run on the set level). | 20 | 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 |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| usher_clades | File | The clades predicted for the samples |
| usher_phb_analysis_date | String | The date the analysis was run |
| usher_phb_version | String | The version of PHB the workflow is from |
| usher_protobuf_version | String | The version of the mutation-annotated protobuf tree (what day and what samples are included, if a default organism was used; otherwise, says it was user-provided) |
| usher_subtree_mutations | Array[File] | An array of files showing the mutations at each internal node for the subtree |
| usher_subtrees | Array[File] | An array of subtrees where your samples have been placed |
| usher_uncondensed_tree | File | The entire global tree with your samples included (warning: may be a very large file if the organism is "sars-cov-2") |
| usher_version | String | The version of UShER used |