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

The Pangolin_Update workflow updates prior Pangolin lineage calls for each sample to meet the lineage calls specified in an alternative docker image. The most common use case for this is updating lineage calls to be up-to-date with the latest Pangolin nomenclature, by using the latest available Pangolin docker image (found here).

User Inputs

Outputs

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