Overview Table
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Any Taxa¶
| Name | Description | Taxa | Workflow Level | Command-line Compatible1 | 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 |
| 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 |
| Concatenate_Illumina_Lanes | Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | Concatenate_Illumina_Lanes_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 | |
| Fetch_SRR_Accession | Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | Fetch_SRR_Accession_PHB |
| Kraken2 | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | Kraken2_PE_PHB, Kraken2_SE_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 |
| SRA_Fetch | Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | SRA_Fetch_PHB |
| TheiaMeta | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | TheiaMeta_Illumina_PE_PHB |
| TheiaValidate | This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | No | v2.0.0 | TheiaValidate_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 |
Bacteria¶
| Name | Description | Applicable Kingdom | Workflow Level | Command-line Compatibility1 | Last Known Changes | Dockstore |
|---|---|---|---|---|---|---|
| Core_Gene_SNP | Pangenome analysis | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | Core_Gene_SNP_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 |
| GAMBIT_Query | Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | Gambit_Query_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 |
| NCBI-AMRFinderPlus | Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | NCBI-AMRFinderPlus_PHB |
| Snippy_Streamline | Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | v2.3.0 | 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 | v2.3.0 | 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 | v2.3.0 | Snippy_Tree_PHB |
| Snippy_Variants | Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | Snippy_Variants_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 | v2.3.0 | TBProfiler_tNGS_PHB |
| Terra_2_NCBI | Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | Terra_2_NCBI_PHB |
| TheiaProk Workflow Series | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | v2.3.0 | TheiaProk_Illumina_PE_PHB, TheiaProk_Illumina_SE_PHB, TheiaProk_ONT_PHB, TheiaProk_FASTA_PHB |
Mycotics¶
| 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 |
| 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 |
| GAMBIT_Query | Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | Gambit_Query_PHB |
| kSNP3 | SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | kSNP3_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 |
| NCBI-AMRFinderPlus | Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | NCBI-AMRFinderPlus_PHB |
| Snippy_Variants | Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | Snippy_Variants_PHB |
| Terra_2_NCBI | Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | Terra_2_NCBI_PHB |
| TheiaEuk | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.3.0 | TheiaEuk_Illumina_PE_PHB |
Viral¶
| 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 | v2.3.0 | Augur_Prep_PHB, Augur_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 |
| Freyja Workflow Series | Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.3.0 | Freyja_FASTQ_PHB, Freyja_Plot_PHB, Freyja_Dashboard_PHB, Freyja_Update_PHB |
| kSNP3 | SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | v2.1.0 | kSNP3_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 |
| 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 | v2.3.0 | Mercury_Prep_N_Batch_PHB |
| Pangolin_Update | Update Pangolin assignments | SARS-CoV-2, Viral | Sample-level | Yes | v2.0.0 | Pangolin_Update_PHB |
| 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 |
| Snippy_Variants | Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.3.0 | Snippy_Variants_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 | v2.3.0 | Terra_2_NCBI_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 | v2.3.0 | TheiaCoV_Illumina_PE_PHB, TheiaCoV_Illumina_SE_PHB, TheiaCoV_ONT_PHB, TheiaCoV_ClearLabs_PHB, TheiaCoV_FASTA_PHB, TheiaCoV_FASTA_Batch_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 |
| VADR_Update | Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v2.2.0 | VADR_Update_PHB |