Page Contents

Workflows available

Assembly_Fetch

Augur

BaseSpace_Fetch

Cauris_CladeTyper

Concatenate_Column_Content

Core_Gene_SNP

CZGenEpi_Prep

Find_Shared_Variants

Freyja Wastewater Analysis Series

GAMBIT_Query

Kraken2

kSNP3

Lyve_SET

MashTree_FASTA

Mercury_Prep_N_Batch

Pangolin Update

RASUSA

Rename_FASTQ

Snippy_Streamline

Snippy_Tree

Snippy_Variants

SRA_Fetch

TBProfiler_tNGS

Terra_2_GISAID

Terra_2_NCBI

TheiaCoV Workflow Series

TheiaEuk Workflow Series

TheiaMeta Workflow Series

TheiaProk Workflow Series

TheiaValidate

Transfer_Column_Content

Usher_PHB

VADR_Update

Zip_Column_Content

Guide to Phylogenetics

Overview

The SRA_Fetch workflow downloads sequence data from NCBI’s Sequence Read Archive (SRA). It requires an SRA run accession then populates the associated read files to a Terra data table.

Inputs

Tasks/Actions

Outputs

References

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