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Database and Docker Versions

Throughout this repository, we have carefully selected a number of default databases and Docker images that are intended to be sufficient starting points for most analyses. The following tables describe the default values for all databases, Docker images, and reference files used throughout the suite of PHB workflows.

Default Databases

Terra Task Name Variable Type Description Default Value Workflow
checkv_consensus checkv_db File CheckV database file gs://theiagen-public-resources-rp/reference_data/databases/checkv/checkv-db-v1.5.tar.gz TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo checkv_db File CheckV database file gs://theiagen-public-resources-rp/reference_data/databases/checkv/checkv-db-v1.5.tar.gz TheiaViral_Illumina_PE, TheiaViral_ONT
gambit gambit_db_genomes File Database of metadata for assembled query genomes; requires complementary signatures file. If not provided, uses default database "/gambit-db" gs://gambit-databases-rp/2.1.0/gambit-metadata-2.1.0-20250808.gdb Gambit_Query, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit gambit_db_signatures File Signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. gs://gambit-databases-rp/2.1.0/gambit-signatures-2.1.0-20250808.gs Gambit_Query, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma gamma_db File Multifasta sequence database GAMMA is to use for gene matching gs://theiagen-public-resources-rp/reference_data/databases/gamma/default_ResFinderDB_Combined_05-06-20.fsa TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder kmerfinder_db File Bacterial database for KmerFinder gs://theiagen-public-resources-rp/reference_data/databases/kmerfinder/kmerfinder_bacteria_20230911.tar.gz TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kraken2 kraken2_db File The database used to run Kraken2 gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz NCBI_Scrub_PE, NCBI_Scrub_SE
kraken2_dehosted kraken2_db File The database used to run Kraken2. Must contain viral and human sequences. gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz TheiaCoV_ClearLabs
kraken2_raw kraken2_db File The database used to run Kraken2. Must contain viral and human sequences. gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz TheiaCoV_ClearLabs
merlin_magic poppunk_gps_clusters_csv File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_clusters.csv TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_dists_npy File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.npy TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_dists_pkl File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.pkl TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_external_clusters_csv File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_external_clusters.csv TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_fit_npz File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.npz TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_fit_pkl File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.pkl TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_graph_gt File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_graph.gt TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_h5 File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.h5 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_qcreport_txt File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_qcreport.txt TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_refs File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_refs_dists_npy File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.npy TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_refs_dists_pkl File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.pkl TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_refs_graph_gt File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6refs_graph.gt TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_refs_h5 File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.h5 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_gps_unword_clusters_csv File Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_unword_clusters.csv TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic virulencefinder_database String The specific database to use virulence_ecoli TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
metabuli metabuli_db File Metabuli database file gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz TheiaViral_ONT
read_QC_trim kraken_db File A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database. Must contain human and viral sequences gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
read_QC_trim midas_db File The database used by the MIDAS task in .tar.gz format gs://theiagen-public-files-rp/terra/theiaprok-files/midas/midas_db_v1.2.tar.gz TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
referenceseeker referenceseeker_db File Database used by the referenceseeker tool that contains bacterial genomes from RefSeq release 205. Downloaded from the referenceseeker GitHub repository. gs://theiagen-public-resources-rp/reference_data/databases/referenceseeker/referenceseeker-bacteria-refseq-205.v20210406.tar.gz Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA
skani skani_db File Skani database file gs://theiagen-public-resources-rp/reference_data/databases/skani/skani_db_20250613.tar TheiaViral_Illumina_PE, TheiaViral_ONT
theiaeuk_illumina_pe gambit_db_genomes File User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db" gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb TheiaEuk_Illumina_PE
theiaeuk_illumina_pe gambit_db_signatures File User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs TheiaEuk_Illumina_PE
theiaeuk_ont gambit_db_genomes File User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db" gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb TheiaEuk_ONT
theiaeuk_ont gambit_db_signatures File User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs TheiaEuk_ONT
theiameta_illumina_pe kraken2_db File A Kraken2 database in .tar.gz format gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_standard_08gb_20230605.tar.gz TheiaMeta_Illumina_PE
theiaprok_fasta abricate_db String Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB vfdb TheiaProk_FASTA
theiaprok_fasta bakta_db String Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation. full TheiaProk_FASTA
theiaprok_illumina_pe abricate_db String Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB vfdb TheiaProk_Illumina_PE
theiaprok_illumina_pe bakta_db String Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation. full TheiaProk_Illumina_PE
theiaprok_illumina_se abricate_db String Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB vfdb TheiaProk_Illumina_SE
theiaprok_illumina_se bakta_db String Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation. full TheiaProk_Illumina_SE
theiaprok_ont abricate_db String Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB vfdb TheiaProk_ONT
theiaprok_ont bakta_db String Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation. full TheiaProk_ONT
theiaviral_illumina_pe kraken_db File Kraken2 database file gs://theiagen-public-resources-rp/reference_data/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz TheiaViral_Illumina_PE
vadr_update vadr_model_file File Path to the a tar + gzipped VADR model file gs://theiagen-public-resources-rp/reference_data/databases/vadr_models/vadr-models-sarscov2-1.3-2.tar.gz VADR_Update

Default Docker Images

All Docker variables are String types with the description: "The Docker container to use for the task".

Terra Task Name Variable Default Value Workflow
abricate docker us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
add_biosample_accessions docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Terra_2_NCBI
amr_search docker us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 AMR_Search
amrfinderplus_nuc docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.23-2025-07-16.1 AMRFinderPlus
amrfinderplus_task docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.23-2025-07-16.1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani docker us-docker.pkg.dev/general-theiagen/staphb/mummer:4.0.0-rgdv2 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_stats docker us-docker.pkg.dev/general-theiagen/theiagen/arln_stats:1.0.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
assembled_reads_percent docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 TheiaMeta_Illumina_PE
augur_align docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_ancestral docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_clades docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_export docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_refine docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_traits docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_translate docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
augur_tree docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
bakta docker us-docker.pkg.dev/general-theiagen/staphb/bakta:1.10.3 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bam_to_unaligned_fastq docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 Host_Decontaminate
bcftools_consensus docker us-docker.pkg.dev/general-theiagen/staphb/bcftools:1.20 TheiaViral_ONT
biosample_submit_tsv_ftp_upload docker us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10 Terra_2_NCBI
busco docker us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.7.1_cv1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bwa docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE
calculate_coverage docker us-docker.pkg.dev/general-theiagen/staphb/bedtools:2.31.0 TheiaMeta_Illumina_PE
calculate_coverage_paf docker us-docker.pkg.dev/general-theiagen/quay/ubuntu:latest TheiaMeta_Illumina_PE
cat_files docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Augur, Concatenate_Column_Content
cat_files_fasta docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 TheiaCoV_FASTA_Batch
cat_lanes docker us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2 Concatenate_Illumina_Lanes
cat_ont_barcodes docker us-docker.pkg.dev/general-theiagen/theiagen/ont-barcodes:0.0.2 ONT_Barcode_Concatenation
cat_variants docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Find_Shared_Variants
centroid docker us-docker.pkg.dev/general-theiagen/theiagen/centroid:0.1.0 Snippy_Streamline, Snippy_Streamline_FASTA
cg_pipeline_clean docker us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
cg_pipeline_raw docker us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
cg_reorder_matrix docker us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Snippy_Tree
checkv_consensus docker us-docker.pkg.dev/general-theiagen/staphb/checkv:1.0.3 TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo docker us-docker.pkg.dev/general-theiagen/staphb/checkv:1.0.3 TheiaViral_Illumina_PE, TheiaViral_ONT
chroquetas docker us-docker.pkg.dev/general-theiagen/theiagen/chroquetas:1.0.0 ChroQueTas
chunk_files docker us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Dorado_Basecalling
cladetyper docker us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Cauris_CladeTyper
clair3 docker us-docker.pkg.dev/general-theiagen/theiagen/clair3-extra-models:1.0.10 TheiaViral_ONT
clair3_variants_ont clair3_docker us-docker.pkg.dev/general-theiagen/staphb/clair3:1.0.10 Clair3_Variants_ONT
clean_check_reads docker us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
compare_two_tsvs docker us-docker.pkg.dev/general-theiagen/theiagen/theiavalidate:1.1.2 TheiaValidate
concatenate_qc_metrics docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Snippy_Tree
concatenate_variants docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Snippy_Tree
consensus docker us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019-epi2me TheiaCoV_ONT
consensus docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaViral_Illumina_PE
consensus_qc docker us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT, VADR_Update
core_iqtree docker us-docker.pkg.dev/general-theiagen/staphb/iqtree:1.6.7 Core_Gene_SNP
core_reorder_matrix docker us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Core_Gene_SNP, kSNP3, kSNP4
core_snp_dists docker us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Core_Gene_SNP, kSNP3, kSNP4
core_snp_sites docker us-docker.pkg.dev/general-theiagen/staphb/snp-sites:2.5.1 Core_Gene_SNP
create_table_from_array docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 Dorado_Basecalling
create_terra_table docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 ONT_Barcode_Concatenation
czgenepi_wrangling docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-08-2 CZGenEpi_Prep
digger_denovo bwa_docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
digger_denovo filter_contigs_docker us-docker.pkg.dev/general-theiagen/theiagen/shovilter:0.2 TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
digger_denovo megahit_docker us-docker.pkg.dev/general-theiagen/theiagen/megahit:1.2.9 TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
digger_denovo pilon_docker us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0 TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
digger_denovo skesa_docker us-docker.pkg.dev/general-theiagen/staphb/skesa:2.4.0 TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
digger_denovo spades_docker us-docker.pkg.dev/general-theiagen/staphb/spades:4.1.0 TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
dorado_basecall docker us-docker.pkg.dev/general-theiagen/staphb/dorado:0.9.0-cuda12.2.0 Dorado_Basecalling
dorado_demux docker us-docker.pkg.dev/general-theiagen/staphb/dorado:0.9.0-cuda12.2.0 Dorado_Basecalling
dorado_trim docker us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.3 Dorado_Basecalling
download_accession docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:16.38.1 Host_Decontaminate
download_terra_table docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 CZGenEpi_Prep, Mercury_Prep_N_Batch, Terra_2_ENA
export_taxon_table docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
export_two_tsvs docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 TheiaValidate
fasta_to_ids docker ubuntu Augur
fasta_utilities docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 TheiaViral_ONT
fastq_scan_clean_reads docker us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3 TheiaCoV_ClearLabs
fastq_scan_raw_reads docker us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3 TheiaCoV_ClearLabs
fetch_bs docker us-docker.pkg.dev/general-theiagen/theiagen/basespace_cli:1.2.1 BaseSpace_Fetch
fetch_sra_to_fastq docker us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0 SRA_Fetch
fetch_srr docker us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0 Fetch_SRR_Accession
filter_sequences_by_length docker us-docker.pkg.dev/general-theiagen/broadinstitute/viral-core:2.1.33 Augur
find_files docker us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine Dorado_Basecalling
flu_track abricate_flu_docker us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-insaflu-220727 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_track assembly_metrics_docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_track genoflu_docker us-docker.pkg.dev/general-theiagen/staphb/genoflu:1.06 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_track irma_docker_image us-docker.pkg.dev/general-theiagen/staphb/irma:1.2.0 TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_track nextclade_docker_image us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.14.5 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_track nextclade_output_parser_docker us-docker.pkg.dev/general-theiagen/python/python:3.8.18-slim TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flye docker us-docker.pkg.dev/general-theiagen/staphb/flye:2.9.4 TheiaViral_ONT
freyja docker us-docker.pkg.dev/general-theiagen/staphb/freyja:1.5.3 Freyja_FASTQ
freyja_dashboard_task docker us-docker.pkg.dev/general-theiagen/staphb/freyja:1.5.3 Freyja_Dashboard
freyja_plot_task docker us-docker.pkg.dev/general-theiagen/staphb/freyja:1.5.3 Freyja_Plot
freyja_update_refs docker us-docker.pkg.dev/general-theiagen/staphb/freyja:1.5.3 Freyja_Update
gambit docker us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0 Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma docker us-docker.pkg.dev/general-theiagen/staphb/gamma:2.2 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gene_coverage docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
get_fasta_genome_size docker us-docker.pkg.dev/general-theiagen/biocontainers/seqkit:2.4.0--h9ee0642_0 Freyja_FASTQ
gisaid_upload docker us-docker.pkg.dev/general-theiagen/broadinstitute/gisaid-cli:3.0 Terra_2_GISAID
ivar_consensus ivar_bwa_docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_consensus ivar_consensus_docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_consensus ivar_trim_primers_docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_consensus ivar_variant_docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_consensus stats_n_coverage_docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_consensus stats_n_coverage_primtrim_docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
ivar_variants docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan TheiaViral_Illumina_PE
kmerfinder docker us-docker.pkg.dev/general-theiagen/biocontainers/kmerfinder:3.0.2--hdfd78af_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kraken2 docker_image us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db NCBI_Scrub_PE, NCBI_Scrub_SE
kraken2_clean docker us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db TheiaMeta_Illumina_PE
kraken2_dehosted docker_image us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db TheiaCoV_ClearLabs
kraken2_pe docker us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db Kraken_PE
kraken2_raw docker us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db TheiaMeta_Illumina_PE
kraken2_raw docker_image us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db TheiaCoV_ClearLabs
kraken2_recalculate_abundances docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-28-v4 Kraken_ONT
kraken2_se docker us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db Kraken_ONT, Kraken_SE
krona docker us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 Kraken_PE, Kraken_SE
krona_clean docker us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 TheiaMeta_Illumina_PE
krona_raw docker us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 TheiaMeta_Illumina_PE
ksnp3_task docker_image us-docker.pkg.dev/general-theiagen/staphb/ksnp3:3.1 kSNP3
ksnp4_task docker_image us-docker.pkg.dev/general-theiagen/staphb/ksnp4:4.1 kSNP4
lyveset docker_image us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f Lyve_SET
make_table docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 Create_Terra_Table
mashtree_task docker us-docker.pkg.dev/general-theiagen/staphb/mashtree:1.2.0 MashTree_FASTA
mask_low_coverage docker us-docker.pkg.dev/general-theiagen/staphb/bedtools:2.31.0 TheiaViral_ONT
megahit docker us-docker.pkg.dev/general-theiagen/theiagen/megahit:1.2.9 TheiaViral_Illumina_PE
mercury docker us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.1.3 Mercury_Prep_N_Batch
merlin_magic abricate_abaum_docker_image us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic abricate_vibrio_docker_image us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic agrvate_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic amr_search_docker_image us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic chroquetas_docker_image TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic clockwork_docker_image us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic ectyper_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/ectyper:1.0.0--pyhdfd78af_1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic emmtyper_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/emmtyper:0.2.0--py_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic emmtypingtool_docker_image us-docker.pkg.dev/general-theiagen/staphb/emmtypingtool:0.0.1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic genotyphi_docker_image us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.11.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic hicap_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/hicap:1.0.3--py_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic kaptive_docker_image us-docker.pkg.dev/general-theiagen/staphb/kaptive:2.0.3 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic kleborate_docker_image us-docker.pkg.dev/general-theiagen/staphb/kleborate:2.2.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic legsta_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/legsta:0.5.1--hdfd78af_2 TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic lissero_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/lissero:0.4.9--py_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic meningotype_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/meningotype:0.8.5--pyhdfd78af_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic ngmaster_docker_image us-docker.pkg.dev/general-theiagen/staphb/ngmaster:1.0.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic pasty_docker_image us-docker.pkg.dev/general-theiagen/staphb/pasty:1.0.3 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic pbptyper_docker_image us-docker.pkg.dev/general-theiagen/staphb/pbptyper:1.0.4 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic poppunk_docker_image us-docker.pkg.dev/general-theiagen/staphb/poppunk:2.4.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic seqsero2s_docker_image us-docker.pkg.dev/general-theiagen/staphb/seqsero2s:1.1.4 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic seroba_docker_image us-docker.pkg.dev/general-theiagen/staphb/seroba:1.0.2 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic serotypefinder_docker_image us-docker.pkg.dev/general-theiagen/staphb/serotypefinder:2.0.1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic shigatyper_docker_image us-docker.pkg.dev/general-theiagen/staphb/shigatyper:2.0.5 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic shigeifinder_docker_image us-docker.pkg.dev/general-theiagen/staphb/shigeifinder:1.3.5 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic sistr_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic snippy_gene_query_docker_image us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic snippy_variants_docker_image us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0 TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic sonneityping_docker_image us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic spatyper_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/spatyper:0.3.3--pyhdfd78af_3 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic srst2_docker_image us-docker.pkg.dev/general-theiagen/staphb/srst2:0.2.0-vcholerae TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic staphopia_sccmec_docker_image us-docker.pkg.dev/general-theiagen/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic stxtyper_docker_image us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.42 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic tbp_parser_docker_image us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.6.0 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic tbprofiler_docker_image us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
merlin_magic vibecheck_docker_image watronfire/vibecheck:2025.02.24 TheiaProk_Illumina_PE
merlin_magic virulencefinder_docker_image us-docker.pkg.dev/general-theiagen/staphb/virulencefinder:2.0.4 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
metabuli docker us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.0 TheiaViral_ONT
metaspades_pe docker us-docker.pkg.dev/general-theiagen/biocontainers/spades:3.12.0--h9ee0642_3 TheiaMeta_Illumina_PE
minimap2 docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT
minimap2_assembly docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 TheiaMeta_Illumina_PE
minimap2_assembly_correction docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 TheiaMeta_Illumina_PE
minimap2_ont docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 Host_Decontaminate
minimap2_pe docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 Host_Decontaminate
minimap2_reads docker us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22 TheiaMeta_Illumina_PE
morgana_magic abricate_flu_docker us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-insaflu-220727 TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic assembly_metrics_docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic genoflu_docker us-docker.pkg.dev/general-theiagen/staphb/genoflu:1.06 TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic irma_docker_image us-docker.pkg.dev/general-theiagen/staphb/irma:1.2.0 TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic nextclade_docker_image us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.10.2 TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic nextclade_output_parser_docker us-docker.pkg.dev/general-theiagen/python/python:3.8.18-slim TheiaViral_Illumina_PE, TheiaViral_ONT
morgana_magic pangolin_docker_image us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.10.2 TheiaViral_Illumina_PE, TheiaViral_ONT
mutation_context docker us-docker.pkg.dev/general-theiagen/theiagen/nextstrain-mpox-mutation-context:2024-06-27 Augur
nanoplot_clean docker us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0 Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_raw docker us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0 Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoq docker us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1 TheiaViral_ONT
ncbi_datasets docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:16.38.1 TheiaViral_Illumina_PE, TheiaViral_ONT
ncbi_datasets_download_genome_accession docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:16.38.1 Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA
ncbi_identify docker us-docker.pkg.dev/general-theiagen/theiagen/ncbi-datasets:18.9.0-python-jq Host_Decontaminate, TheiaViral_Illumina_PE, TheiaViral_ONT
ncbi_scrub_pe docker us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1 NCBI_Scrub_PE
ncbi_scrub_se docker us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1 NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaViral_ONT
ncbi_sftp_upload docker us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10 Terra_2_NCBI
nextclade_output_parser docker us-docker.pkg.dev/general-theiagen/python/python:3.8.18-slim TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
nextclade_v3 docker us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.16.0 TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
nextclade_v3_set docker us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.14.5 Nextclade_Batch
organism_parameters pangolin_docker_image us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34 Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA
pan_iqtree docker us-docker.pkg.dev/general-theiagen/staphb/iqtree:1.6.7 Core_Gene_SNP
pan_reorder_matrix docker us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Core_Gene_SNP, kSNP3, kSNP4
pan_snp_dists docker us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Core_Gene_SNP, kSNP3, kSNP4
pangolin_update_log docker us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Pangolin_Update
parse_mapping docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 Host_Decontaminate, TheiaViral_ONT
phylovalidate_task docker us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.1.8 PhyloCompare
pilon docker us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0 TheiaMeta_Illumina_PE
pirate docker_image us-docker.pkg.dev/general-theiagen/biocontainers/pirate:1.0.5--hdfd78af_0 Core_Gene_SNP
plasmidfinder docker us-docker.pkg.dev/general-theiagen/staphb/plasmidfinder:2.1.6 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
porechop docker us-docker.pkg.dev/general-theiagen/staphb/porechop:0.2.4 TheiaViral_ONT
prep_augur_metadata docker us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Augur_Prep
primer_trim docker us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan Freyja_FASTQ
prokka docker us-docker.pkg.dev/general-theiagen/staphb/prokka:1.14.5 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
prune_table docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Terra_2_NCBI
qc_check_task docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
quasitools_illumina_pe docker us-docker.pkg.dev/general-theiagen/biocontainers/quasitools:0.7.0--pyh864c0ab_1 TheiaCoV_Illumina_PE
quasitools_ont docker us-docker.pkg.dev/general-theiagen/biocontainers/quasitools:0.7.0--pyh864c0ab_1 TheiaCoV_ONT
quast docker us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2 TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
quast_denovo docker us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2 TheiaViral_Illumina_PE, TheiaViral_ONT
rasusa docker us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0 TheiaViral_Illumina_PE, TheiaViral_ONT
rasusa_task docker us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0 RASUSA, TheiaEuk_Illumina_PE
raven docker us-docker.pkg.dev/general-theiagen/theiagen/raven:1.8.3 TheiaViral_ONT
raw_check_reads docker us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
read_QC_trim artic_guppyplex_docker us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3 TheiaCoV_ONT
read_QC_trim kraken2_recalculate_abundances_docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-28-v4 TheiaCoV_ONT, TheiaProk_ONT
read_QC_trim kraken_docker_image us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db TheiaCoV_ONT, TheiaProk_ONT
read_QC_trim nanoq_docker us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1 TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT
read_QC_trim ncbi_scrub_docker us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1 TheiaCoV_ONT
read_QC_trim rasusa_docker us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0 TheiaProk_ONT
read_QC_trim_ont kraken2_recalculate_abundances_docker Freyja_FASTQ
read_mapping_stats docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 Host_Decontaminate, TheiaViral_Illumina_PE, TheiaViral_ONT
referenceseeker docker us-docker.pkg.dev/general-theiagen/biocontainers/referenceseeker:1.8.0--pyhdfd78af_0 Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA
register_ena_samples docker us-docker.pkg.dev/general-theiagen/theiagen/terra_to_ena:0.6 Terra_2_ENA
rename_PE_files docker us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816 Rename_FASTQ
rename_SE_files docker us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816 Rename_FASTQ
reorder_matrix docker us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Augur, MashTree_FASTA
resfinder_task docker us-docker.pkg.dev/general-theiagen/staphb/resfinder:4.1.11 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
retrieve_aligned_contig_paf docker us-docker.pkg.dev/general-theiagen/biocontainers/seqkit:2.4.0--h9ee0642_0 TheiaMeta_Illumina_PE
retrieve_aligned_pe_reads_sam docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 TheiaMeta_Illumina_PE
retrieve_unaligned_pe_reads_sam docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 TheiaMeta_Illumina_PE
root_tree1_task docker us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.1.8 PhyloCompare
root_tree2_task docker us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.1.8 PhyloCompare
sam_to_sorted_bam docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE
samtools_faidx docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 Clair3_Variants_ONT
sc2_defaults docker us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0 Augur
semibin docker us-docker.pkg.dev/general-theiagen/biocontainers/semibin:2.0.2--pyhdfd78af_0 TheiaMeta_Illumina_PE
shared_variants docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Find_Shared_Variants, Snippy_Tree
skani docker us-docker.pkg.dev/general-theiagen/staphb/skani:0.2.2 TheiaViral_Illumina_PE, TheiaViral_ONT
sm_theiacov_fasta_wrangling docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-28-v4 TheiaCoV_FASTA_Batch
snippy_gene_query docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 Snippy_Variants
snippy_tree_wf gubbins_docker us-docker.pkg.dev/general-theiagen/biocontainers/gubbins:3.3--py310pl5321h8472f5a_0 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree
snippy_tree_wf iqtree2_docker us-docker.pkg.dev/general-theiagen/staphb/iqtree2:2.1.2 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree
snippy_tree_wf snippy_core_docker us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree
snippy_tree_wf snp_dists_docker us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree
snippy_tree_wf snp_sites_docker us-docker.pkg.dev/general-theiagen/staphb/snp-sites:2.5.1 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree
snippy_variants_wf docker us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0 Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants
snp_dists docker us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2 Augur
sort_bam_assembly_correction docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17 TheiaMeta_Illumina_PE
spades docker us-docker.pkg.dev/general-theiagen/staphb/spades:4.1.0 TheiaViral_Illumina_PE
sra_tsv_to_xml docker us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10 Terra_2_NCBI
stats_n_coverage docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_ClearLabs, TheiaCoV_ONT
stats_n_coverage_primtrim docker us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 TheiaCoV_ClearLabs, TheiaCoV_ONT
submit_ena_data docker us-docker.pkg.dev/general-theiagen/theiagen/terra_to_ena:0.6 Terra_2_ENA
summarize_data docker us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16 Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4
table2asn docker us-docker.pkg.dev/general-theiagen/staphb/ncbi-table2asn:1.26.678 Mercury_Prep_N_Batch
tbp_parser docker us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.9.1 TBProfiler_tNGS
tbprofiler docker us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3 TBProfiler_tNGS
theiacov_clearlabs medaka_docker us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3 TheiaCoV_ClearLabs
theiacov_fasta_batch pangolin_docker us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34 TheiaCoV_FASTA_Batch
theiacov_illumina_pe pangolin_docker_image us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34 TheiaCoV_Illumina_PE
theiacov_illumina_se pangolin_docker_image us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34 TheiaCoV_Illumina_SE
theiacov_ont pangolin_docker_image us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34 TheiaCoV_ONT
theiaeuk_illumina_pe busco_docker_image us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1 TheiaEuk_Illumina_PE
theiaeuk_ont busco_docker_image us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1 TheiaEuk_ONT
transfer_files docker us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine Freyja_Update
transfer_files docker_image us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine Transfer_Column_Content
trim_genbank_fastas docker us-docker.pkg.dev/general-theiagen/staphb/vadr:1.3 Mercury_Prep_N_Batch
trimmomatic_pe docker us-docker.pkg.dev/general-theiagen/staphb/trimmomatic:0.39 TBProfiler_tNGS
ts_mlst docker us-docker.pkg.dev/general-theiagen/staphb/mlst:2.23.0-2024-12-31 TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
tsv_join docker us-docker.pkg.dev/general-theiagen/broadinstitute/viral-core:2.1.33 Augur
usher docker us-docker.pkg.dev/general-theiagen/pathogengenomics/usher:0.6.2 Usher
vadr docker us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.4 TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update
version_capture docker us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0 AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, ChroQueTas, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4
wg_reorder_matrix docker us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1 Snippy_Tree
zip_files docker_image us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1 Zip_Column_Content

Default References

Terra Task Name Variable Type Description Default Value Workflow
augur reference_fasta File The reference FASTA file used to align the genomes and build the trees Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl. For an organism without set defaults, a reference fasta file must be provided otherwise the workflow fails. Augur
augur reference_genbank File The GenBank .gb file for the same reference genome used for the reference_fasta Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl. For an organism without set defaults, a reference genbank file must be provided otherwise the workflow fails. Augur
cladetyper ref_clade1 File The reference assembly for clade 1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.fasta Cauris_CladeTyper
cladetyper ref_clade1_annotated String The path to the annotated reference for clade 1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.gbff Cauris_CladeTyper
cladetyper ref_clade2 File The reference assembly for clade 2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta Cauris_CladeTyper
cladetyper ref_clade2_annotated String The path to the annotated reference for clade 2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff Cauris_CladeTyper
cladetyper ref_clade3 File The reference assembly for clade 3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta Cauris_CladeTyper
cladetyper ref_clade3_annotated String The path to the annotated reference for clade 3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff Cauris_CladeTyper
cladetyper ref_clade4 File The reference assembly for clade 4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta Cauris_CladeTyper
cladetyper ref_clade4_annotated String The path to the annotated reference for clade 4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff Cauris_CladeTyper
cladetyper ref_clade5 File The reference assembly for clade 5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta Cauris_CladeTyper
cladetyper ref_clade5_annotated String The path to the annotated reference for clade 5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff Cauris_CladeTyper
cladetyper ref_clade6 File The reference assembly for clade 6 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta Cauris_CladeTyper
merlin_magic cladetyper_ref_clade1 File Reference genome FASTA for Candidozyma auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.2_Cand_auris_B8441_V2_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade1_annotated File Reference GBFF annotation for C. auris clade1 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435_Cauris_B8441_V2_genomic.gbff TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade2 File Reference genome FASTA for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade2_annotated File Reference GBFF annotation for C. auris clade2 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade3 File Reference genome FASTA for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade3_annotated File Reference GBFF annotation for C. auris clade3 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade4 File Reference genome FASTA for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade4_annotated File Reference GBFF annotation for C. auris clade4 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade5 File Reference genome FASTA for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade5_annotated File Reference GBFF annotation for C. auris clade5 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade6 File Reference genome FASTA for C. auris clade6 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta TheiaEuk_Illumina_PE, TheiaEuk_ONT
merlin_magic cladetyper_ref_clade6 File The reference assembly for clade 6 gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
nextclade_batch input_ref File An optional FASTA file containing reference sequence. This file should contain exactly 1 sequence Uses the reference fasta associated with the specified nextclade dataset name Nextclade_Batch
nextclade_batch reference_tree_json File An optional phylogenetic reference tree file which serves as a target for phylogenetic placement Uses the reference tree associated with the specified nextclade dataset name Nextclade_Batch
nextclade_v3 auspice_reference_tree_json File An Auspice JSON phylogenetic reference tree which serves as a target for phylogenetic placement. Inherited from nextclade dataset TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
nextclade_v3 input_ref File A nucleotide sequence which serves as a reference for the pairwise alignment of all input sequences. This is also the sequence which defines the coordinate system of the genome annotation. See here for more info: https://docs.nextstrain.org/projects/nextclade/en/latest/user/input-files/02-reference-sequence.html Inherited from nextclade dataset TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
organism_parameters reference_gff_file File Reference GFF file for the organism being analyzed Default provided for mpox ("gs://theiagen-public-resources-rp/reference_data/viral/mpox/Mpox-MT903345.1.reference.gff3") and HIV (primer versions 1 ["gs://theiagen-public-resources-rp/reference_data/viral/hiv/NC_001802.1.gff3"] and 2 ["gs://theiagen-public-resources-rp/reference_data/viral/hiv/AY228557.1.gff3"]) Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_ONT