Usher¶

Quick Facts¶

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level	Dockstore
Phylogenetic Placement	Monkeypox virus, SARS-CoV-2, Viral	v2.1.0	Yes	Sample-level, Set-level	Usher_PHB

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 your samples in FASTA format; 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	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	cpu	Int	Number of CPUs to allocate to the task	4	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	16	Optional
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