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

<aside> ⚠️ If the Terra_2_NCBI workflow fails, DO NOT resubmit. ⚠️⚠️ ⚠️ ⚠️ ⚠️⚠️ ⚠️

Resubmission risks duplicate submissions and future failures.

Contact Theiagen ([email protected]) to determine the reason for failure, and only move forward with Theiagen’s guidance.

⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️ ⚠️

</aside>

<aside> 🗝️ Key resources

Terra_2_NCBI-PATHOGEN-metadata-2023-12-28.xlsx

Terra_2_NCBI-MICROBE-metadata-2022-07-11.xlsx

Terra_2_NCBI-VIRUS-metadata-2022-09-09.xlsx

</aside>

The Terra_2_NCBI workflow is a programmatic data submission method to share metadata information with NCBI BioSample and paired-end Illumina reads with NCBI SRA directly from Terra without having to use the NCBI portal.

Prerequisites

Collating BioSample Metadata

Running the Workflow

Limitations

Acknowledgments

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