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.
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 |