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Data Import

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Assembly_Fetch Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly Any taxa Sample-level Yes v1.3.0 Assembly_Fetch_PHB
BaseSpace_Fetch Import data from BaseSpace into Terra Any taxa Sample-level Yes v2.0.0 BaseSpace_Fetch_PHB
Create_Terra_Table Upload data to Terra and then run this workflow to have the table automatically created Any taxa Yes v2.2.0 Create_Terra_Table_PHB
SRA_Fetch Import publicly available reads from SRA using SRR#, ERR# or DRR# Any taxa Sample-level Yes v2.2.0 SRA_Fetch_PHB

Genomic Characterization

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Freyja Workflow Series Recovers relative lineage abundances from mixed sample data and generates visualizations SARS-CoV-2, Viral Sample-level, Set-level Yes v2.2.0 Freyja_FASTQ_PHB, Freyja_Plot_PHB, Freyja_Dashboard_PHB, Freyja_Update_PHB
Pangolin_Update Update Pangolin assignments SARS-CoV-2, Viral Sample-level Yes v2.0.0 Pangolin_Update_PHB
TheiaCov Workflow Series Viral genome assembly, QC and characterization from amplicon sequencing HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV Sample-level, Set-level Some optional features incompatible, Yes v2.2.0 TheiaCoV_Illumina_PE_PHB, TheiaCoV_Illumina_SE_PHB, TheiaCoV_ONT_PHB, TheiaCoV_ClearLabs_PHB, TheiaCoV_FASTA_PHB, TheiaCoV_FASTA_Batch_PHB
TheiaEuk Mycotic genome assembly, QC and characterization from WGS data Mycotics Sample-level Some optional features incompatible, Yes v2.0.1 TheiaEuk_Illumina_PE_PHB
TheiaMeta Genome assembly and QC from metagenomic sequencing Any taxa Sample-level Yes v2.0.0 TheiaMeta_Illumina_PE_PHB
TheiaProk Workflow Series Bacterial genome assembly, QC and characterization from WGS data Bacteria Sample-level Some optional features incompatible, Yes v2.2.0 TheiaProk_Illumina_PE_PHB, TheiaProk_Illumina_SE_PHB, TheiaProk_ONT_PHB, TheiaProk_FASTA_PHB
VADR_Update Update VADR assignments HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV Sample-level Yes v1.2.1 VADR_Update_PHB

Phylogenetic Construction

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Augur Phylogenetic analysis for viral pathogens Viral Sample-level, Set-level Yes v2.1.0 Augur_Prep_PHB, Augur_PHB
Core_Gene_SNP Pangenome analysis Bacteria Set-level Some optional features incompatible, Yes v2.1.0 Core_Gene_SNP_PHB
CZGenEpi_Prep Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. Monkeypox virus, SARS-CoV-2, Viral Set-level No v1.3.0 CZGenEpi_Prep_PHB
Find_Shared_Variants Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples Bacteria, Mycotics Set-level Yes v2.0.0 Find_Shared_Variants_PHB
kSNP3 SNP-based phylogenetic analysis from assemblies Bacteria, Mycotics, Viral Set-level Some optional features incompatible, Yes v2.1.0 kSNP3_PHB
Lyve_SET Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis Bacteria Set-level Yes v2.1.0 Lyve_SET_PHB
MashTree_FASTA Mash-distance based phylogenetic analysis from assemblies Bacteria, Mycotics, Viral Set-level Some optional features incompatible, Yes v2.1.0 MashTree_FASTA_PHB
Snippy_Streamline Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection Bacteria Set-level Yes v2.2.0 Snippy_Streamline_PHB
Snippy_Streamline_FASTA Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection Bacteria Set-level Yes v2.2.0 Snippy_Streamline_FASTA_PHB
Snippy_Tree SNP-based phylogenetic analysis from reads, with option to mask recombination Bacteria Set-level Some optional features incompatible, Yes v2.1.0 Snippy_Tree_PHB
Snippy_Variants Alignment of reads to a reference genome, then SNP calling Bacteria, Mycotics, Viral Sample-level Yes v2.2.0 Snippy_Variants_PHB

Phylogenetic Placement

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Samples_to_Ref_Tree Use Nextclade to rapidly and accurately place your samples on any existing phylogenetic tree Monkeypox virus, SARS-CoV-2, Viral Sample-level, Set-level Yes v2.1.0 Samples_to_Ref_Tree_PHB
Usher_PHB Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree Monkeypox virus, SARS-CoV-2, Viral Sample-level, Set-level Yes v2.1.0 Usher_PHB

Public Data Sharing

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Mercury_Prep_N_Batch Prepare metadata and sequence data for submission to NCBI and GISAID Influenza, Monkeypox virus, SARS-CoV-2, Viral Set-level No v2.2.0 Mercury_Prep_N_Batch_PHB
Terra_2_GISAID Upload of assembly data to GISAID SARS-CoV-2, Viral Set-level Yes v1.2.1 Terra_2_GISAID_PHB
Terra_2_NCBI Upload of sequence data to NCBI Bacteria, Mycotics, Viral Set-level No v2.1.0 Terra_2_NCBI_PHB

Exporting Data from Terra

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Concatenate_Column_Content Concatenate contents of a specified Terra data table column for many samples ("entities") Any taxa Set-level Yes v2.1.0 Concatenate_Column_Content_PHB
Transfer_Column_Content Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location Any taxa Set-level Yes v1.3.0 Transfer_Column_Content_PHB
Zip_Column_Content Zip contents of a specified Terra data table column for many samples ("entities") Any taxa Set-level Yes v2.1.0 Zip_Column_Content_PHB

Standalone

Name Description Applicable Kingdom Workflow Level Command-line Compatibility1 Last Known Changes Dockstore
Cauris_CladeTyper C. auris clade assignment Mycotics Sample-level Yes v1.0.0 Cauris_CladeTyper_PHB
GAMBIT_Query Taxon identification of genome assembly using GAMBIT Bacteria, Mycotics Sample-level Yes v2.0.0 Gambit_Query_PHB
Kraken2 Taxa identification from reads Any taxa Sample-level Yes v2.0.0 Kraken2_PE_PHB, Kraken2_SE_PHB
NCBI-AMRFinderPlus Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) Bacteria, Mycotics Sample-level Yes v2.0.0 NCBI-AMRFinderPlus_PHB
NCBI_Scrub Runs NCBI's HRRT on Illumina FASTQs Any taxa Sample-level Yes v2.2.1 NCBI_Scrub_PE_PHB, NCBI_Scrub_SE_PHB
RASUSA Randomly subsample sequencing reads to a specified coverage Any taxa Sample-level Yes v2.0.0 RASUSA_PHB
Rename_FASTQ Rename paired-end or single-end read files in a Terra data table in a non-destructive way Any taxa Sample-level Yes v2.1.0 Rename_FASTQ_PHB
TBProfiler_tNGS Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser Bacteria, TB Sample-level Yes v2.0.0 TBProfiler_tNGS_PHB
TheiaValidate This workflow performs basic comparisons between user-designated columns in two separate tables. Any taxa No v2.0.0 TheiaValidate_PHB

  1. Command-line compatibility is determined if the workflow can be run on a local command-line environment, providing all dependencies are installed, with either miniwdl or cromwell