Page Contents

Workflows available

Assembly_Fetch

Augur

Concatenate_Column_Content

Core_Gene_SNP

CZGenEpi_Prep

Freyja Wastewater Analysis

Kraken2

kSNP3

Lyve_SET

MashTree_FASTA

Mercury_Prep_N_Batch

Pangolin Update

Rasusa

Snippy_Streamline

Snippy_Tree

Snippy_Variants

SRA_Fetch

Terra_2_GISAID

Terra_2_NCBI

TheiaCoV Genomic Characterization

TheiaEuk

TheiaMeta

TheiaProk Workflow Series

TheiaValidate

The Guide to Phylogenetics

Usher_PHB

VADR_Update

Zip_Column_Content

Overview

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 Inputs

Outputs

Terra Outputs

References

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