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Available Standard Operating Procedures

Theiagen has developed a number of Standard Operating Procedures (SOPs) to help you analyze your data. Please see the available SOPs below.

All SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Analyze SARS-COV-2 using TheiaCoV_FASTA v2 FASTA, TheiaCoV v1 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_PE_PHB v4 PE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_SE_PHB v4 SE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_ONT v4 ONT, TheiaCoV v3 SC2 Current
Analyzing Bacterial Data in Terra using Theiagen’s TheiaProk Illumina PE Workflow v3 PE, TheiaProk v2, v3 Bacterial Current
Analyzing SARS-CoV-2 Metagenomic Samples using Freyja FASTQ v2 Freyja v2 SC2 Current
Analyzing SARS-CoV-2 using TheiaCov_ClearLabs v4 CL, TheiaCoV v3 SC2 Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v1 TheiaValidate v1, v2 Validations Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v3 TheiaValidate v2, v3 Validations Current
Creating Static Reference Files for Freyja Analysis in Terra using Freyja Update v2 Freyja v2 SC2 Current
Creating a Dashboard Visualization of SARS-CoV-2 Metagenomic Samples using Freyja Dashboard v2 Freyja v2 SC2 Current
Getting Started In Terra v4 None v2, v3 Getting Started Current
Linking BaseSpace and Importing BaseSpace Reads to Terra v3 BaseSpace_Fetch v3 Data Import Current
Plotting SARS-CoV-2 Metagenomic Sample Data using Freyja Plot v3 Freyja v2 SC2 Current
Running Influenza A, H3N2 Metagenomic Samples in Terra using Theiagen’s Freyja FASTQ Workflow v1 Freyja v3 Flu Current
Running Theiagen’s Rasusa Workflow in Terra to Randomly Downsample Reads v2 RASUSA v1, v2 Downsampling Current
Running Theiagen’s Snippy_Variants_PHB Workflow in Terra v1 Snippy_Variants v2 Bacterial, Phylogenetic construction Current
Submitting SC2 Sequence Data to GISAID using Theiagen’s Terra 2 GISAID Workflow v2 Terra_2_GISAID v2 Public data sharing, SC2 Current
TheiaProk_ONT v3 ONT, TheiaProk v2, v3 Bacterial Current
Uploading Data, Creating Metadata Tables and TSV files, and Importing Workflows v4 None v3 Data Import Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_PE_PHB v3 PE, TheiaCoV v2 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_Illumina_SE_PHB v3 SE, TheiaCoV v2 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_ONT v2 ONT, TheiaCoV v1 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_ONT v3 ONT, TheiaCoV v2 SC2 Prior
Analyzing Bacterial Data in Terra using Theiagen’s TheiaProk Illumina PE Workflow v2 PE, TheiaProk v1 Bacterial Prior
Analyzing Flu Data in Terra using TheiaCov_Illumina_PE and Augur Workflows v1 Augur, PE, TheiaCoV v1 Flu, Phylogenetic construction Prior
Analyzing HAI Pathogens using Phoenix Version 1 in Terra v1 Phoenix v1 HAI Prior
Analyzing HAI Pathogens using Phoenix Version 2 in Terra v1 Phoenix v1 HAI Prior
Analyzing Phylogenetic Relationships in Terra using Theiagen’s Augur Workflows v1 Augur v1 Phylogenetic construction Prior
Analyzing SARS-CoV-2 using TheiaCov_ClearLabs v3 CL, TheiaCoV v2 SC2 Prior
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v2 TheiaValidate v2 Validations Prior
Getting Started In Terra v3 None v2, v3 Getting Started Prior
Linking BaseSpace and Importing BaseSpace Reads to Terra v2 BaseSpace_Fetch v2 Data Import Prior
TheiaProk_ONT v2 ONT, TheiaProk v1 Bacterial Prior
Uploading Data, Creating Metadata Tables and TSV files, and Importing Workflows v3 None v1, v2 Data Import Prior

Most Up-to-Date SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Analyze SARS-COV-2 using TheiaCoV_FASTA v2 FASTA, TheiaCoV v1 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_PE_PHB v4 PE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_SE_PHB v4 SE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_ONT v4 ONT, TheiaCoV v3 SC2 Current
Analyzing Bacterial Data in Terra using Theiagen’s TheiaProk Illumina PE Workflow v3 PE, TheiaProk v2, v3 Bacterial Current
Analyzing SARS-CoV-2 Metagenomic Samples using Freyja FASTQ v2 Freyja v2 SC2 Current
Analyzing SARS-CoV-2 using TheiaCov_ClearLabs v4 CL, TheiaCoV v3 SC2 Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v1 TheiaValidate v1, v2 Validations Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v3 TheiaValidate v2, v3 Validations Current
Creating Static Reference Files for Freyja Analysis in Terra using Freyja Update v2 Freyja v2 SC2 Current
Creating a Dashboard Visualization of SARS-CoV-2 Metagenomic Samples using Freyja Dashboard v2 Freyja v2 SC2 Current
Getting Started In Terra v4 None v2, v3 Getting Started Current
Linking BaseSpace and Importing BaseSpace Reads to Terra v3 BaseSpace_Fetch v3 Data Import Current
Plotting SARS-CoV-2 Metagenomic Sample Data using Freyja Plot v3 Freyja v2 SC2 Current
Running Influenza A, H3N2 Metagenomic Samples in Terra using Theiagen’s Freyja FASTQ Workflow v1 Freyja v3 Flu Current
Running Theiagen’s Rasusa Workflow in Terra to Randomly Downsample Reads v2 RASUSA v1, v2 Downsampling Current
Running Theiagen’s Snippy_Variants_PHB Workflow in Terra v1 Snippy_Variants v2 Bacterial, Phylogenetic construction Current
Submitting SC2 Sequence Data to GISAID using Theiagen’s Terra 2 GISAID Workflow v2 Terra_2_GISAID v2 Public data sharing, SC2 Current
TheiaProk_ONT v3 ONT, TheiaProk v2, v3 Bacterial Current
Uploading Data, Creating Metadata Tables and TSV files, and Importing Workflows v4 None v3 Data Import Current

Data Import SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Linking BaseSpace and Importing BaseSpace Reads to Terra v3 BaseSpace_Fetch v3 Data Import Current
Uploading Data, Creating Metadata Tables and TSV files, and Importing Workflows v4 None v3 Data Import Current
Linking BaseSpace and Importing BaseSpace Reads to Terra v2 BaseSpace_Fetch v2 Data Import Prior
Uploading Data, Creating Metadata Tables and TSV files, and Importing Workflows v3 None v1, v2 Data Import Prior

Viral SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Analyze SARS-COV-2 using TheiaCoV_FASTA v2 FASTA, TheiaCoV v1 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_PE_PHB v4 PE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_SE_PHB v4 SE, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_ONT v4 ONT, TheiaCoV v3 SC2 Current
Analyzing SARS-CoV-2 using TheiaCov_ClearLabs v4 CL, TheiaCoV v3 SC2 Current
Analyze SARS-COV-2 using TheiaCoV_Illumina_PE_PHB v3 PE, TheiaCoV v2 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_Illumina_SE_PHB v3 SE, TheiaCoV v2 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_ONT v2 ONT, TheiaCoV v1 SC2 Prior
Analyze SARS-COV-2 using TheiaCoV_ONT v3 ONT, TheiaCoV v2 SC2 Prior
Analyzing Flu Data in Terra using TheiaCov_Illumina_PE and Augur Workflows v1 Augur, PE, TheiaCoV v1 Flu, Phylogenetic construction Prior
Analyzing SARS-CoV-2 using TheiaCov_ClearLabs v3 CL, TheiaCoV v2 SC2 Prior

Bacterial SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Analyzing HAI Pathogens using Phoenix Version 1 in Terra v1 Phoenix v1 HAI Prior
Analyzing HAI Pathogens using Phoenix Version 2 in Terra v1 Phoenix v1 HAI Prior

Phylogenetic SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Running Theiagen’s Snippy_Variants_PHB Workflow in Terra v1 Snippy_Variants v2 Bacterial, Phylogenetic construction Current
Analyzing Flu Data in Terra using TheiaCov_Illumina_PE and Augur Workflows v1 Augur, PE, TheiaCoV v1 Flu, Phylogenetic construction Prior
Analyzing Phylogenetic Relationships in Terra using Theiagen’s Augur Workflows v1 Augur v1 Phylogenetic construction Prior

Data Sharing SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Submitting SC2 Sequence Data to GISAID using Theiagen’s Terra 2 GISAID Workflow v2 Terra_2_GISAID v2 Public data sharing, SC2 Current

Miscellaneous SOPs

SOP SOP version Workflow PHB version compatibility Pathogen/Category Current or prior wf version?
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v1 TheiaValidate v1, v2 Validations Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v3 TheiaValidate v2, v3 Validations Current
Running Theiagen’s Rasusa Workflow in Terra to Randomly Downsample Reads v2 RASUSA v1, v2 Downsampling Current
Running Theiagen’s Snippy_Variants_PHB Workflow in Terra v1 Snippy_Variants v2 Bacterial, Phylogenetic construction Current
Comparing Terra Data Tables using Theiagen’s TheiaValidate Workflow v2 TheiaValidate v2 Validations Prior