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Name Description Applicable Kingdom Workflow Level Workflow Type Command-line Compatibility Last Known Changes Dockstore
[**AMR_Search**](../workflows/standalone/amr_search.md) Perform AMR profiling on microbial assemblies mimicing Pathogenwatch [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v3.0.1 [AMR_Search_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/AMR_Search_PHB:fc-amr-search-dev?tab=info)
[**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Data Import](../../workflows_overview/workflows_type.md#data-import) Yes v3.1.0 [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info)
[**Augur**](../workflows/phylogenetic_construction/augur.md) Phylogenetic analysis for viral pathogens [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level, Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v4.1.0 [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info)
[**BaseSpace_Fetch**](../workflows/data_import/basespace_fetch.md) Import data from BaseSpace into Terra [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Data Import](../../workflows_overview/workflows_type.md#data-import) Yes v4.0.0 [BaseSpace_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/BaseSpace_Fetch_PHB:main?tab=info)
[**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md) C. auris clade assignment [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v4.0.0 [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info)
[**Clair3_Variants**](../workflows/phylogenetic_construction/clair3_variants.md) ONT Variant Caller [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v4.1.0 [Clair3_Variants_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Clair3_Variants_ONT_PHB:main?tab=info)
[**Concatenate_Column_Content**](../workflows/data_export/concatenate_column_content.md) Concatenate contents of a specified Terra data table column for many samples ("entities") [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Set-level [Exporting Data from Terra](../../workflows_overview/workflows_type.md#exporting-data-from-terra) Yes v2.1.0 [Concatenate_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Column_Content_PHB:main?tab=info)
[**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md) Concatenate Illumina lanes for a single sample [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v2.3.0 [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info)
[**Core_Gene_SNP**](../workflows/phylogenetic_construction/core_gene_snp.md) Pangenome analysis [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [Core_Gene_SNP_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Core_Gene_SNP_PHB:main?tab=info)
[**Create_Terra_Table**](../workflows/data_import/create_terra_table.md) Upload data to Terra and then run this workflow to have the table automatically created [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) [Data Import](../../workflows_overview/workflows_type.md#data-import) No v2.2.0 [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info)
[**CZGenEpi_Prep**](../workflows/phylogenetic_construction/czgenepi_prep.md) Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. Monkeypox virus, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v1.3.0 [CZGenEpi_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/CZGenEpi_Prep_PHB:main?tab=info)
[**Dorado_Basecalling**](../workflows/standalone/dorado_basecalling.md) GPU-accelerated basecalling of Oxford Nanopore sequencing data [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) No v3.0.1 [Dorado_Basecalling_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Dorado_Basecalling_PHB:main?tab=info)
[**Fetch_SRR_Accession**](../workflows/data_import/fetch_srr_accession.md) Provided a BioSample accession, identify any associated SRR accession(s) [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Data Import](../../workflows_overview/workflows_type.md#data-import) Yes v2.3.0 [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info)
[**Find_Shared_Variants**](../workflows/phylogenetic_construction/find_shared_variants.md) Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v2.0.0 [Find_Shared_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Find_Shared_Variants_PHB:main?tab=info)
[**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md) Recovers relative lineage abundances from mixed sample data and generates visualizations SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level, Set-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Yes vX.X.X [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info)
[**GAMBIT_Query**](../workflows/standalone/gambit_query.md) Taxon identification of genome assembly using GAMBIT [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v2.0.0 [Gambit_Query_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Gambit_Query_PHB:main?tab=info)
[**Kraken2**](../workflows/standalone/kraken2.md) Taxa identification from reads [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v3.1.0 [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info), [Kraken2_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_ONT_PHB:main?tab=info)
[**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md) SNP-based phylogenetic analysis from assemblies [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info)
[**kSNP4**](../workflows/phylogenetic_construction/ksnp4.md) SNP-based phylogenetic analysis from assemblies [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes vX.X.X [kSNP4_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP4_PHB:main?tab=info)
[**Lyve_SET**](../workflows/phylogenetic_construction/lyve_set.md) Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v4.1.0 [Lyve_SET_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Lyve_SET_PHB:main?tab=info)
[**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md) Mash-distance based phylogenetic analysis from assemblies [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info)
[**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md) Prepare metadata and sequence data for submission to NCBI and GISAID Influenza, Monkeypox virus, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Public Data Sharing](../../workflows_overview/workflows_type.md#public-data-sharing) No v4.0.0 [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info)
[**Metabuli**](../workflows/standalone/metabuli.md) Taxa identification from reads, including ONT data [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes vX.X.X [Metabuli_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Metabuli_PHB:main?tab=info)
[**Microreact_Export**](../workflows/data_export/microreact_export.md) Generate Microreact upload files from a Terra data table [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Set-level [Exporting Data from Terra](../../workflows_overview/workflows_type.md#exporting-data-from-terra) Yes vX.X.X [Microreact_Export_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Microreact_Export_PHB:main?tab=info)
[**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md) Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v4.1.0 [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info)
[**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md) Runs NCBI's HRRT on Illumina FASTQs [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v2.2.1 [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info)
[**Nextclade_Batch**](../workflows/phylogenetic_placement/nextclade_batch.md) Use Nextclade to rapidly and accurately place your samples on any existing phylogenetic tree Monkeypox virus, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Phylogenetic Placement](../../workflows_overview/workflows_type.md#phylogenetic-placement) Yes v4.0.0 [Nextclade_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Nextclade_Batch_PHB:main?tab=info)
[**ONT_Barcode_Concatenation**](../workflows/data_import/ont_barcode_concatenation.md) Creates a Terra table after concatenating barcodes from ONT data [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) [Data Import](../../workflows_overview/workflows_type.md#data-import) No v4.0.0 [ONT_Barcode_Concatenation_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/ONT_Barcode_Concatenation_PHB:main?tab=info)
[**Pangolin_Update**](../workflows/genomic_characterization/pangolin_update.md) Update Pangolin assignments SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Yes v3.0.1 [Pangolin_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Pangolin_Update_PHB:main?tab=info)
[**PhyloCompare**](../workflows/standalone/phylocompare.md) Quantify the difference between two phylogenetic trees with the same tips Any taxa Sample-level Standalone Yes v4.0.0 [PhyloCompare_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/PhyloCompare_PHB:main?tab=info)
[**RASUSA**](../workflows/standalone/rasusa.md) Randomly subsample sequencing reads to a specified coverage [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v3.0.0 [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info)
[**Rename_FASTQ**](../workflows/standalone/rename_fastq.md) Rename paired-end or single-end read files in a Terra data table in a non-destructive way [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v2.1.0 [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info)
[**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md) Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info)
[**Snippy_Streamline_FASTA**](../workflows/phylogenetic_construction/snippy_streamline_fasta.md) Implementation of Snippy workflows for phylogenetic analysis from assembled genomes (in FASTA format), with optional dynamic reference selection [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [Snippy_Streamline_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_FASTA_PHB:im-snippy-fasta-dev?tab=info)
[**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md) SNP-based phylogenetic analysis from reads, with option to mask recombination [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Set-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Some optional features incompatible, Yes v4.1.0 [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info)
[**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md) Alignment of reads to a reference genome, then SNP calling [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level [Phylogenetic Construction](../../workflows_overview/workflows_type.md#phylogenetic-construction) Yes v2.3.0 [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info)
[**SRA_Fetch**](../workflows/data_import/sra_fetch.md) Import publicly available reads from SRA using SRR#, ERR# or DRR# [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Data Import](../../workflows_overview/workflows_type.md#data-import) Yes v2.2.0 [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info)
[**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md) Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), TB Sample-level [Standalone](../../workflows_overview/workflows_type.md#standalone) Yes v4.1.0 [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:main?tab=info)
[**Terra_2_ENA**](../workflows/public_data_sharing/terra_2_ena.md) Upload of sequence data to ENA [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level Public Data Sharing No v3.1.0 [Terra_2_ENA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_ENA_PHB:main?tab=info)
[**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md) Upload of assembly data to GISAID SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Public Data Sharing](../../workflows_overview/workflows_type.md#public-data-sharing) Yes v1.2.1 [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info)
[**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md) Upload of sequence data to NCBI [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md#viral) Set-level [Public Data Sharing](../../workflows_overview/workflows_type.md#public-data-sharing) No v4.0.0 [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info)
[**TheiaCov Workflow Series**](../workflows/genomic_characterization/theiacov.md) Viral genome assembly, QC and characterization from amplicon sequencing HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral), WNV Sample-level, Set-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Some optional features incompatible, Yes vX.X.X [TheiaCoV_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_PE_PHB:main?tab=info), [TheiaCoV_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_SE_PHB:main?tab=info), [TheiaCoV_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ONT_PHB:main?tab=info), [TheiaCoV_ClearLabs_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ClearLabs_PHB:main?tab=info), [TheiaCoV_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_PHB:main?tab=info), [TheiaCoV_FASTA_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_Batch_PHB:main?tab=info)
[**TheiaEuk Workflow Series**](../workflows/genomic_characterization/theiaeuk.md) Mycotic genome assembly, QC and characterization from WGS data [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Some optional features incompatible, Yes vX.X.X [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info), [TheiaEuk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_ONT_PHB:main?tab=info)
[**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) Genome assembly and QC from metagenomic sequencing [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Yes vX.X.X [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info)
[**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) Bacterial genome assembly, QC and characterization from WGS data [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria) Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Some optional features incompatible, Yes vX.X.X [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info)
[**TheiaValidate**](../workflows/standalone/theiavalidate.md) This workflow performs basic comparisons between user-designated columns in two separate tables. [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) [Standalone](../../workflows_overview/workflows_type.md#standalone) No v3.0.0 [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info)
[**TheiaViral Workflow Series**](../workflows/genomic_characterization/theiaviral.md) Viral genome assembly, QC, and characterization from WGS or hybrid-capture panel data. [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Some optional features incompatible, Yes vX.X.X [TheiaViral_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaViral_Illumina_PE_PHB:main?tab=info), [TheiaViral_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaViral_ONT_PHB:main?tab=info), [TheiaViral_Panel_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaViral_Panel_PHB:main?tab=info)
[**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md) Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Set-level [Exporting Data from Terra](../../workflows_overview/workflows_type.md#exporting-data-from-terra) Yes v1.3.0 [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info)
[**Usher**](../workflows/phylogenetic_placement/usher.md) Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree Monkeypox virus, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral) Sample-level, Set-level [Phylogenetic Placement](../../workflows_overview/workflows_type.md#phylogenetic-placement) Yes v2.1.0 [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info)
[**VADR_Update**](../workflows/genomic_characterization/vadr_update.md) Update VADR assignments HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, [Viral](../../workflows_overview/workflows_kingdom.md#viral), WNV Sample-level [Genomic Characterization](../../workflows_overview/workflows_type.md#genomic-characterization) Yes v4.0.0 [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info)
[**Zip_Column_Content**](../workflows/data_export/zip_column_content.md) Zip contents of a specified Terra data table column for many samples ("entities") [Any taxa](../../workflows_overview/workflows_kingdom.md#any-taxa) Set-level [Exporting Data from Terra](../../workflows_overview/workflows_type.md#exporting-data-from-terra) Yes v2.1.0 [Zip_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Zip_Column_Content_PHB:main?tab=info)