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all_outputs.tsv
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Variable Type Description Workflow
abricate_abaum_database String Database of reference A. baumannii plasmid typing genes used for plasmid typing TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_abaum_docker String Docker file used for running abricate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_abaum_plasmid_tsv File <https://github.com/tseemann/abricate#output> containing a row for each A. baumannii plasmid type gene found in the sample TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_abaum_plasmid_type_genes String A. baumannii Plasmid typing genes found in the sample; from GENE column in <https://github.com/tseemann/abricate#output> TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_abaum_version String Version of abricate used for A. baumannii plasmid typing TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_database String Database of reference used with Abricate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_docker String Docker file used for running abricate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_flu_database String ABRicate database used for analysis TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
abricate_flu_results File File containing all results from ABRicate TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
abricate_flu_subtype String Flu subtype as determined by ABRicate TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
abricate_flu_type String Flu type as determined by ABRicate TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
abricate_flu_version String Version of ABRicate TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
abricate_genes String Genes found in the sample; from GENE column in <https://github.com/tseemann/abricate#output> TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_results_tsv File <https://github.com/tseemann/abricate#output> containing a row for each gene found in the sample TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_version String Version of abricate used for A. baumannii plasmid typing TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_biotype String Biotype classification according to tcpA gene sequence (Classical or ElTor) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_ctxA String Presence or absence of the ctxA gene TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_database String Database to use while running abricate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_detailed_tsv File Detailed ABRicate output file TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_docker String Docker file used for running abricate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_ompW String Presence or absence of the ompW gene TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_serogroup String Serotype classification as O1 (wbeN gene), O139 (wbfR gene) or not detected. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_toxR String Presence or absence of the toxR gene TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
abricate_vibrio_version String The abricate version run TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_agr_canonical String Canonical or non-canonical agrD TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_agr_group String Agr group TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_agr_match_score String Match score for agr group TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_agr_multiple String If multiple agr groups were found TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_agr_num_frameshifts String Number of frameshifts found in CDS of extracted agr operon TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_docker String The docker used for AgrVATE TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_results File A gzipped tarball of all results TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_summary File The summary file produced TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
agrvate_version String The version of AgrVATE used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
aligned_bai String Index companion file to the bam file generated during the consensus assembly process Freyja_FASTQ, TheiaCoV_Illumina_PE
aligned_bai File Index companion file to the bam file generated during the consensus assembly process Clair3_Variants_ONT, TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, TheiaCoV_ONT
aligned_bam String Sorted BAM file containing the alignments of reads to the reference genome Freyja_FASTQ, TheiaCoV_Illumina_PE
aligned_bam File Sorted BAM file containing the alignments of reads to the reference genome Clair3_Variants_ONT, TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, TheiaCoV_ONT
aligned_fai File Index file for the reference genome Clair3_Variants_ONT
alignment_method String The method used to generate the alignment Freyja_FASTQ
amr_results_csv File CSV formatted AMR profile AMR_Search
amr_results_pdf File PDF formatted AMR profile AMR_Search
amr_search_all_resistances String All resistances returned by AMRsearch AMR_Search, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_associated_resistances String Resistances paired with their agent returned by AMRsearch AMR_Search, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_csv File CSV formatted AMR profile TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_docker String Docker image used to run AMR_Search AMR_Search, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_results File JSON formatted AMR profile including BLAST results AMR_Search, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_results_pdf File PDF formatted AMR profile TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_version String Version of AMR_Search libraries used AMR_Search, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amr_search_wf_analysis_date String Date of analysis AMR_Search
amr_search_wf_version String Version of PHB used for analysis AMR_Search
amrfinderplus_all_report File Output TSV file from AMRFinderPlus (described <https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#fields>) AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_betalactam_genes String Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to beta-lactams TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_carbapenem_genes String Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to carbapenem TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_cephalosporin_genes String Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to cephalosporin TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_cephalothin_genes String Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to cephalothin TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_genes String Beta-lactam AMR genes identified by AMRFinderPlus TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_betalactam_methicillin_genes String Beta-lactam AMR genes identified by AMRFinderPlus that are known to confer resistance to methicilin TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_classes String AMRFinderPlus predictions for classes of drugs that genes found in the reads are known to confer resistance to AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_core_genes String AMR genes identified by AMRFinderPlus where the scope is "core" AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_plus_genes String AMR genes identified by AMRFinderPlus where the scope is "plus" AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_report File TSV file detailing AMR genes only, from the amrfinderplus_all_report AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_amr_subclasses String More specificity about the drugs that genes identified in the reads confer resistance to AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_db_version String AMRFinderPlus database version used AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_stress_genes String Stress genes identified by AMRFinderPlus AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_stress_report File TSV file detailing stress genes only, from the amrfinderplus_all_report AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_version String AMRFinderPlus version used AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_virulence_genes String Virulence genes identified by AMRFinderPlus AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_virulence_report File TSV file detailing virulence genes only, from the amrfinderplus_all_report AMRFinderPlus, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
amrfinderplus_wf_analysis_date String Date of analysis AMRFinderPlus
amrfinderplus_wf_version String Version of PHB used for the analysis AMRFinderPlus
ani_highest_percent Float Highest ANI between query and any given reference genome (top species match) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani_highest_percent_bases_aligned Float Percentage of bases aligned between query genome and top species match TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani_mummer_docker String Docker image used to run the ANI_mummer task TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani_mummer_version String Version of MUMmer used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani_output_tsv File Full output TSV from ani-m TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ani_top_species_match String Species of genome with highest ANI to query FASTA TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_assembly_ratio String Assembly ratio of the final assembly compared to the mean assembly length of the taxon. These stats are gathered from a statistics file created by the CDC aggregating NCBI assembly data by taxon. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_assembly_zscore String ZScore of the samples assembly length to assess the uniformity of the assembly when compared to taxon means. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_r1_q30_clean String Q30% of the cleaned R1 FASTQ TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_r1_q30_raw String Q30% of the raw R1 FASTQ TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_r2_q30_clean String Q30% of the cleaned R2 FASTQ TheiaProk_Illumina_PE
arln_r2_q30_raw String Q30% of the raw R2 FASTQ TheiaProk_Illumina_PE
arln_stats_docker_version String Docker version for task_arln_stats.wdl TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_taxon_assembly_ratio_stdev String Reported assembely length standard deviation of the given taxonomy pulled from NCBI aggregated data. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_taxon_gc_mean String Mean GC percent of the taxon. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
arln_taxon_gc_percent_stdev String Reported GC percent standard deviation of the given taxonomy pulled from NCBI aggregated data. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
artic_docker String Docker image utilized for read trimming and consensus genome assembly TheiaCoV_ClearLabs, TheiaCoV_ONT
artic_version String Version of the Artic software utilized for read trimming and conesnsus genome assembly TheiaCoV_ClearLabs, TheiaCoV_ONT
assembled_viruses Int Number of viruses assembled from sample TheiaViral_Panel
assembler String Assembler used in digger_denovo subworkflow TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
assembler_version String Version of the assembler used in digger_denovo TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
assemblies Array[File] Assembly files generated during the workflow TheiaViral_Panel
assembly_consensus_fasta File Final consensus assembly in FASTA format TheiaViral_Illumina_PE, TheiaViral_ONT
assembly_denovo_fasta File De novo assembly in FASTA format TheiaViral_Illumina_PE, TheiaViral_ONT
assembly_fasta File _De novo_ genome assembly in FASTA format TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
assembly_fasta String Consensus genome assembly; for lower quality flu samples, the output may state "Assembly could not be generated" when there is too little and/or too low quality data for IRMA to produce an assembly. Contigs will be ordered from largest to smallest when IRMA is used. TheiaCoV_Illumina_PE, TheiaCoV_ONT
assembly_fasta File Consensus genome assembly; for lower quality flu samples, the output may state "Assembly could not be generated" when there is too little and/or too low quality data for IRMA to produce an assembly. Contigs will be ordered from largest to smallest when IRMA is used. TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE
assembly_fasta File The final recovered metagenome-assembled genome (MAG). _"A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables [the identification of] novel species [to] understand their potential functions in a dynamic ecosystem"_[^1] TheiaMeta_Illumina_PE
assembly_fetch_analysis_date String The date the workflow was run Assembly_Fetch
assembly_fetch_ncbi_datasets_assembly_data_report_json File JSON file containing report about assembly downloaded by Asembly_Fetch Assembly_Fetch
assembly_fetch_ncbi_datasets_assembly_fasta File FASTA file downloaded by Assembly_Fetch Assembly_Fetch
assembly_fetch_ncbi_datasets_docker String Docker file used for NCBI datasets Assembly_Fetch
assembly_fetch_ncbi_datasets_gff File Assembly downloaded by Assembly_Fetch in GFF3 format Assembly_Fetch
assembly_fetch_ncbi_datasets_gff3 File Assembly downloaded by Assembly_Fetch in GFF format Assembly_Fetch
assembly_fetch_ncbi_datasets_version String NCBI datasets version used Assembly_Fetch
assembly_fetch_referenceseeker_database String ReferenceSeeker database used Assembly_Fetch
assembly_fetch_referenceseeker_docker String Docker file used for ReferenceSeeker Assembly_Fetch
assembly_fetch_referenceseeker_top_hit_ncbi_accession String NCBI Accession for the top hit identified by Assembly_Fetch Assembly_Fetch
assembly_fetch_referenceseeker_tsv File TSV file of the top hits between the query genome and the Reference Seeker database Assembly_Fetch
assembly_fetch_referenceseeker_version String ReferenceSeeker version used Assembly_Fetch
assembly_fetch_version String The version of the repository the Assembly Fetch workflow is in Assembly_Fetch
assembly_length Int Length of assembly (total contig length) as determined by QUAST TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
assembly_length_unambiguous Int Number of unambiguous basecalls within the consensus assembly TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
assembly_mean_coverage String Mean sequencing depth throughout the consensus assembly. Generated after performing primer trimming and calculated using the SAMtools coverage command TheiaCoV_Illumina_PE, TheiaCoV_ONT
assembly_mean_coverage Float Mean sequencing depth throughout the consensus assembly. Generated after performing primer trimming and calculated using the SAMtools coverage command TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, TheiaMeta_Illumina_PE
assembly_method String Method employed to generate consensus assembly TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
assembly_to_ref_bai File BAM index file for reads aligned to reference TheiaViral_ONT
assembly_to_ref_bam File BAM file of reads aligned to reference TheiaViral_ONT
augur_aligned_fastas File Alignment of inputted FASTAs Augur
augur_auspice_input_json File Auspice-formatted JSON of tree and associated metadata Augur
augur_clade_mutations File Clade-specific mutations identified in the analysis Augur
augur_combined_assemblies File Concatenated FASTAs Augur
augur_distance_tree File Phylogenetic tree without time-calibration Augur
augur_fasttree_version String The fasttree version used, blank if other tree method used Augur
augur_iqtree_model_used String The iqtree model used during augur tree, blank if iqtree not used Augur
augur_iqtree_version String The iqtree version used during augur tree (defualt), blank if other tree method used Augur
augur_keep_list File List of samples that were kept and met length filters Augur
augur_mafft_version String The mafft version used in augur align Augur
augur_metadata File TSV file of the metadata provided as input to the workflow in the proper format for Augur analysis Augur_Prep
augur_metadata_merged File TSV file of merged metadata Augur
augur_phb_analysis_date String The date the analysis was run Augur
augur_phb_version String The version of the Public Health Bioinformatics (PHB) repository used Augur
augur_prep_phb_analysis_date String Date of analysis Augur_Prep
augur_prep_phb_version String Version of the Public Health Bioinformatics (PHB) repository used Augur_Prep
augur_raxml_version String The version of raxml used during augur tree, blank if other tree method used Augur
augur_snp_matrix File SNP matrix generated from alignment Augur
augur_time_tree File Time-calibrated phylogenetic tree Augur
augur_traits_json File JSON of traits used for applying metadata to the phylogenetic tree Augur
augur_version String Version of Augur used Augur
auspice_json File Auspice-compatable JSON output generated from Nextclade analysis that includes the Nextclade default samples for clade-typing and the single sample placed on this tree TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
auspice_json_flu_h5n1 File Auspice-compatable JSON output generated from Nextclade analysis on Influenza H5N1 whole genome that includes the samples included in the "avian-flu/h5n1-cattle-outbreak" nextstrain build that is focused on B3.13 genotype and the single sample placed on this tree TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
auspice_json_flu_ha File Auspice-compatable JSON output generated from Nextclade analysis on Influenza HA segment that includes the Nextclade default samples for clade-typing and the single sample placed on this tree TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
auspice_json_flu_na File Auspice-compatable JSON output generated from Nextclade analysis on Influenza NA segment that includes the Nextclade default samples for clade-typing and the single sample placed on this tree TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
auspice_json_rabies File Auspice-compatable JSON output generated from Nextclade analysis on Rabies virus that includes the Nextclade default samples for clade-typing and the single sample placed on this tree TheiaViral_Illumina_PE, TheiaViral_ONT
average_read_length Float Average read length TheiaMeta_Illumina_PE
bakta_gbff File Genomic GenBank format annotation file TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bakta_gff3 File Generic Feature Format Version 3 file TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bakta_plot File Bakta plot output PNG file summarizing annotated genome features such as coding sequences, RNA genes, and hypothetical proteins. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bakta_summary File Bakta summary output TXT file TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bakta_tsv File Annotations as simple human readable TSV TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bakta_version String Bakta version used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bandage_plot File Image file (PNG) visualizing the Flye assembly graph generated by Bandage TheiaEuk_ONT, TheiaProk_ONT
bandage_version String Version of Bandage used TheiaEuk_ONT, TheiaProk_ONT
bankit_fasta File **Only for mpox submission**: the fasta file that you will use to submit mpox assembly files to NCBI via email Mercury_Prep_N_Batch
bankit_metadata File **Only for mpox submission**: the metadata file that you will use to submit mpox assembly files to NCBI via email Mercury_Prep_N_Batch
bankit_sqn_to_email File **Only for mpox submission**: the sqn file that you will use to submit mpox assembly files to NCBI via email Mercury_Prep_N_Batch
basespace_fetch_analysis_date String The date the workflow was run BaseSpace_Fetch
basespace_fetch_version String The version of the repository the Basespace_Fetch workflow is in BaseSpace_Fetch
bbduk_docker String The Docker image for bbduk, which was used to remove the adapters from the sequences Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
bbduk_primer_stats File Primer trimming statistics TheiaViral_Illumina_PE
bbduk_read1_clean File Clean forward reads after BBDuk processing TheiaViral_Illumina_PE
bbduk_read2_clean File Clean reverse reads after BBDuk processing TheiaViral_Illumina_PE
bcftools_docker String Docker image used for bcftools TheiaViral_ONT
bcftools_filtered_vcf File Filtered variant calls in VCF format from bcftools TheiaViral_ONT
bcftools_version String Version of bcftools used TheiaViral_ONT
bedtools_docker String The Docker image for bedtools, which was used to calculate coverage TheiaMeta_Illumina_PE
bedtools_version String The version of bedtools, which was used to calculate coverage TheiaMeta_Illumina_PE
biosample_failures File Text file listing samples that failed BioSample submission Terra_2_NCBI
biosample_metadata File BioSample metadata TSV file for upload to NCBI Mercury_Prep_N_Batch
biosample_metadata File Metadata used for BioSample submission in proper BioSample formatting Terra_2_NCBI
biosample_report_xmls Array[File] One or more XML files that contain the response from NCBI regarding your BioSample submission. These can be pretty cryptic, but often contain information to determine if anything went wrong Terra_2_NCBI
biosample_status String String showing whether BioSample submission was successful Terra_2_NCBI
biosample_submission_xml File XML file used to submit your BioSamples to NCBI Terra_2_NCBI
bracken_report String Refined kraken2 report generated by Bracken Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE
bracken_report File Refined kraken2 report generated by Bracken Kraken_PE, Kraken_SE
bracken_report_clean String Cleaned refined kraken2 report generated by Bracken TheiaMeta_Illumina_PE
bracken_report_dehosted String Dehosted refined kraken2 report generated by Bracken Freyja_FASTQ, TheiaCoV_Illumina_PE
bracken_report_dehosted File Dehosted refined kraken2 report generated by Bracken TheiaCoV_Illumina_SE
bracken_report_raw File Raw refined kraken2 report generated by Bracken TheiaMeta_Illumina_PE
bracken_version String Version of Bracken used Kraken_PE, Kraken_SE, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE
busco_database String BUSCO database used TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
busco_docker String BUSCO docker image used TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
busco_report File A plain text summary of the results in BUSCO notation TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
busco_results String BUSCO results (see relevant toggle in [this block](https://theiagen.github.io/public_health_bioinformatics/latest/workflows/genomic_characterization/theiaprok/#post-assembly-tasks-performed-for-all-taxa)) TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
busco_version String BUSCO software version used TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
bwa_read1_aligned File Forward reads aligned to reference TheiaViral_Illumina_PE
bwa_read1_unaligned File Forward reads not aligned to reference TheiaViral_Illumina_PE
bwa_read2_aligned File Reverse reads aligned to reference TheiaViral_Illumina_PE
bwa_read2_unaligned File Reverse reads not aligned to reference TheiaViral_Illumina_PE
bwa_samtools_version String Version of samtools used by BWA TheiaViral_Illumina_PE
bwa_sorted_bai File Sorted BAM index file of reads aligned to reference TheiaViral_Illumina_PE
bwa_sorted_bam File Sorted BAM file of reads aligned to reference TheiaViral_Illumina_PE
bwa_sorted_bam_unaligned File A BAM file that only contains reads that did not align to the reference TheiaViral_Illumina_PE
bwa_sorted_bam_unaligned_bai File Index companion file to a BAM file that only contains reads that did not align to the reference TheiaViral_Illumina_PE
bwa_version String Version of BWA software used Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_Illumina_PE
cauris_cladetyper_wf_analysis_date String Date of analysis Cauris_CladeTyper
cauris_cladetyper_wf_version String Version of PHB used for the analysis Cauris_CladeTyper
cg_pipeline_docker String Docker file used for running CG-Pipeline on cleaned reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
cg_pipeline_report_clean File TSV file of read metrics from clean reads, including average read length, number of reads, and estimated genome coverage TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
cg_pipeline_report_raw File TSV file of read metrics from raw reads, including average read length, number of reads, and estimated genome coverage TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
checkv_consensus_contamination File Contamination estimate for consensus assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_status String CheckV runtime status TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_summary File Summary report from CheckV for consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_total_genes String Number of genes detected in consensus assembly by CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_version String Version of CheckV used for consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_weighted_completeness String Weighted completeness score for consensus assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_consensus_weighted_contamination String Weighted contamination score for consensus assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_contamination File Contamination estimate for de novo assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_status String CheckV runtime status TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_summary File Summary report from CheckV for de novo assembly TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_total_genes String Number of genes detected in de novo assembly by CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_version String Version of CheckV used for de novo assembly TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_weighted_completeness String Weighted completeness score for de novo assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
checkv_denovo_weighted_contamination String Weighted contamination score for de novo assembly from CheckV TheiaViral_Illumina_PE, TheiaViral_ONT
cladetype_annotated_ref String The annotated reference file for the identified clade, "None" if no clade was identified/no annotation is inputted TheiaEuk_ONT
cladetyper_annotated_reference String The annotated reference file for the identified clade, "None" if no clade was identified/no annotation is inputted Cauris_CladeTyper, TheiaEuk_Illumina_PE
cladetyper_clade String The clade assigned to the input assembly Cauris_CladeTyper, TheiaEuk_Illumina_PE, TheiaEuk_ONT
cladetyper_docker_image String The Docker container used for the task Cauris_CladeTyper, TheiaEuk_Illumina_PE, TheiaEuk_ONT
cladetyper_gambit_version String The version of GAMBIT used for the analysis Cauris_CladeTyper, TheiaEuk_Illumina_PE
cladetyper_version String The version of Cladetyper used for the analysis TheiaEuk_ONT
clair3_docker String Docker image used for Clair3 TheiaViral_ONT
clair3_docker_image String Version of the Docker container used for Clair3 variant calling Clair3_Variants_ONT
clair3_gvcf File Genomic VCF file from Clair3 TheiaViral_ONT
clair3_model String Model used for Clair3 variant calling TheiaViral_ONT
clair3_model_used String Name of the Clair3 model used for variant calling Clair3_Variants_ONT
clair3_variants_gvcf File Optional genome VCF file containing information about all genomic positions, including non-variant sites Clair3_Variants_ONT
clair3_variants_vcf File Final merged VCF file containing high-confidence variant calls, combining results from both pileup and full-alignment approaches Clair3_Variants_ONT
clair3_variants_wf_version String Version of the PHB workflow used Clair3_Variants_ONT
clair3_vcf File Variant calls in VCF format from Clair3 TheiaViral_ONT
clair3_version String Clair3 Version being used Clair3_Variants_ONT, TheiaViral_ONT
clockwork_decontaminated_read1 File Decontaminated forward reads by Clockwork TBProfiler_tNGS, TheiaProk_Illumina_PE
clockwork_decontaminated_read2 File Decontaminated reverse reads by Clockwork TBProfiler_tNGS, TheiaProk_Illumina_PE
clockwork_version String The version of Clockwork used TBProfiler_tNGS
combined_mean_q_clean Float Mean quality score for the combined clean reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
combined_mean_q_raw Float Mean quality score for the combined raw reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
combined_mean_readlength_clean Float Mean read length for the combined clean reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
combined_mean_readlength_raw Float Mean read length for the combined raw reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
concatenate_column_content_analysis_date String The date the workflow was run Concatenate_Column_Content
concatenate_column_content_version String The version of the repository the workflow is hosted in Concatenate_Column_Content
concatenate_illumina_lanes_analysis_date String Date of analysis Concatenate_Illumina_Lanes
concatenate_illumina_lanes_version String Version of PHB used for the analysis Concatenate_Illumina_Lanes
concatenated_czgenepi_fasta File The concatenated fasta file with the renamed headers (the headers are renamed to account for clearlabs data which has unique headers) CZGenEpi_Prep
concatenated_czgenepi_metadata File The concatenated metadata that was extracted from the terra table using the specified columns CZGenEpi_Prep
concatenated_files File The file containing all of the items from the column you selected. Concatenate_Column_Content
concatenated_variants File The concatenated variants without presence/absence Find_Shared_Variants
consensus_flagstat File Output from the SAMtools flagstat command to assess quality of the alignment file (BAM) TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
consensus_n_variant_min_depth Int Minimum read depth to call variants for iVar consensus and iVar variants. Also represents the minimum consensus support threshold used by IRMA with Illumina Influenza data. TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
consensus_qc_assembly_length_unambiguous Int Length of consensus assembly excluding ambiguous bases TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_qc_number_Degenerate Int Number of degenerate bases in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_qc_number_N Int Number of N bases in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_qc_number_Total Int Total number of bases in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_qc_percent_reference_coverage Float Percent of reference genome covered in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_stats File Output from the SAMtools stats command to assess quality of the alignment file (BAM) TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
contig_number Int The number of contigs in the assembly_fasta (see description for `assembly_fasta`) TheiaMeta_Illumina_PE
contigs_gfa File Assembly graph output generated by SPAdes (Illumina: PE, SE) or Flye (ONT), used to visualize and evaluate genome assembly results. TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
cophylogeny_plot File A cophylogeny plot depicting branching order differences between two phylogenies without branch lengths PhyloCompare
cophylogeny_plot_with_branch_lengths File A cophylogeny plot depicting branching order differences between two phylogenies with branch lengths PhyloCompare
cophylogeny_version String Version of the TheiaPhylo repository used for analysis PhyloCompare
core_gene_snp_wf_analysis_date String Date of analysis using Core_Gene_SNP workflow Core_Gene_SNP
core_gene_snp_wf_version String Version of PHB used for analysis Core_Gene_SNP
czgenepi_prep_analysis_date String The date the workflow was run CZGenEpi_Prep
czgenepi_prep_version String The version of PHB the workflow is in CZGenEpi_Prep
datasets_genome_length_docker String The Docker container used for the task TheiaViral_Illumina_PE, TheiaViral_ONT
datasets_genome_length_version String The version of NCBI Datasets used for analysis TheiaViral_Illumina_PE, TheiaViral_ONT
datatable File Sample-level data table TSV file that was used to update the original sample-level data table in the last step of the TheiaCoV_FASTA_Batch workflow. TheiaCoV_FASTA_Batch
dehost_wf_dehost_read1 File Reads that did not map to host TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_dehost_read2 File Paired-reads that did not map to host TheiaViral_Illumina_PE, TheiaViral_Panel
dehost_wf_host_accession String Host genome accession TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_fasta File Host genome FASTA file TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_flagstat File Output from the SAMtools flagstat command to assess quality of the alignment file (BAM) TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapped_bai File Indexed bam file of the reads aligned to the host reference TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapped_bam File Sorted BAM file containing the alignments of reads to the host reference genome TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_cov_hist File Coverage histogram from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_coverage Float Average coverage from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_mean_depth Float Average depth from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_metrics File File of mapping metrics TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_stats File File of mapping statistics TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_percent_mapped_reads Float Percentage of reads mapped to host reference genome TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dnaapler_version String Version of dnaapler used TheiaEuk_ONT, TheiaProk_ONT
dorado_basecall_docker String Docker image used in the `dorado_basecall` task Dorado_Basecalling
dorado_basecall_version String Version of Dorado used in the `dorado_basecall` task Dorado_Basecalling
dorado_basecalling_analysis_date String Date of Dorado analysis Dorado_Basecalling
dorado_basecalling_phb_version String Version of PHB used for the analysis Dorado_Basecalling
dorado_demux_version String Version of Dorado used in the `dorado_demux` task Dorado_Basecalling
dorado_model_used String Model used for basecalling Dorado_Basecalling
dorado_trim_version String Version of Dorado used in the `dorado_trim` task Dorado_Basecalling
downsampled_read1 File RASUSA downsampled reads derived from read1 input TheiaViral_Illumina_PE
downsampled_read2 File RASUSA downsampled reads derived from read2 input TheiaViral_Illumina_PE
ectyper_database_version String Version of the ECTyper database used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_docker String Docker image used to run ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_pathodb_version String Version of the ECTyper pathotype database used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_pathotype String Samples pathotype predicted by ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_pathotype_count String Number of pathotypes predicted by ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_pathotype_genes String Pathotype genes observed by ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_predicted_serotype String Serotype predicted by ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_qc_result String QC pass or fail for the sample analyzed TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_results File TSV file of evidence for ECTyper predicted serotype (see <https://github.com/phac-nml/ecoli_serotyping#report-format>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_stx_subtypes String Shiga toxin subtypes predicted by ECTyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_version String Version of ECTyper used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ectyper_warnings File ECTyper warning messages TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
emmtyper_docker String Docker image for emmtyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
emmtyper_emm_type String The emm-type of a Streptococcus pyogenes assembly TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
emmtyper_results_tsv File TSV file with emmtyper results TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
emmtyper_version String Version of emmtyper used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
emmtypingtool_docker String Docker image for emm-typing-tool TheiaProk_Illumina_PE
emmtypingtool_emm_type String emm-type predicted TheiaProk_Illumina_PE
emmtypingtool_results_xml File XML file with emm-typing-tool resuls TheiaProk_Illumina_PE
emmtypingtool_version String Version of emm-typing-tool used TheiaProk_Illumina_PE
ena_accessions File Text file containing the accession numbers generated by ENA submission Terra_2_ENA
ena_docker_image String Docker image used for ENA submission processing Terra_2_ENA
ena_excluded_samples File Text file listing samples that were excluded from ENA submission Terra_2_ENA
ena_file_paths_json File JSON file containing paths to the files submitted to ENA Terra_2_ENA
ena_metadata_accessions File File containing metadata and their corresponding accessions from ENA Terra_2_ENA
ena_registration_log File Log file detailing the ENA registration process Terra_2_ENA
ena_registration_success String String indicating whether the ENA registration was successful Terra_2_ENA
ena_registration_summary File Summary file of the ENA registration results Terra_2_ENA
ena_submission_manifest_files Array[File] Array of manifest files used for ENA submission. Each file corresponds to a sample and contains metadata and file paths Terra_2_ENA
ena_submission_report_files Array[File] Array of report files containing the results of the ENA submission Terra_2_ENA
ena_webincli_results File File containing the cumulative results of the ENA submission Terra_2_ENA
est_coverage_clean Float Estimated coverage calculated from clean reads and genome length TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
est_coverage_raw Float Estimated coverage calculated from raw reads and genome length TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
est_genome_length Int Estimated genome length TheiaEuk_ONT
est_percent_gene_coverage_tsv File Percent coverage for each gene in the organism being analyzed (depending on the organism input) Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
ete4_docker String Docker image used for ETE4 taxonomy parsing Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT
ete4_status String Status of standardized taxonomy acquisition TheiaViral_Illumina_PE, TheiaViral_ONT
ete4_version String The version of ETE4 used Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT
excluded_samples File A file that contains the names and reasons why a sample was excluded from submission. **For SARS-CoV-2**, there are two sections: First, a section for any samples that failed to meet pre-determined quality thresholds (`number_N` and `vadr_num_alert`). Second, a section that includes a table that describes any missing required metadata for each sample. This table has the sample name for rows and any columns that have missing metadata as headers. If a sample is missing a piece of required metadata, the corresponding cell will be blank. However, if a different sample does have metadata for that column, the associated value will appear in the corresponding cell. **For flu and mpox**, only the second section described above exists. _Please see the example below for more details_. Mercury_Prep_N_Batch
excluded_samples File Text file listing samples that were excluded from BioSample submission for missing required metadata Terra_2_NCBI
failed_uploads File The metadata for any failed uploads Terra_2_GISAID
fasta_utilities_fai File FASTA index file TheiaViral_ONT
fasta_utilities_samtools_docker String Docker image used for samtools in fasta utilities TheiaViral_ONT
fasta_utilities_samtools_version String Version of samtools used in fasta utilities TheiaViral_ONT
fastp_docker String Docker image used for fastp Freyja_FASTQ, Metabuli, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastp_html_report File The HTML report conveying fastp results Metabuli, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastp_html_report String The HTML report conveying fastp results Freyja_FASTQ
fastp_json_report File The JSON report conveying fastp results Metabuli, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastp_json_report String The JSON report conveying fastp results Freyja_FASTQ
fastp_read1_trimmed File `read1` input trimmed by fastp Metabuli
fastp_read2_trimmed File `read2` input trimmed by fastp Metabuli
fastp_version String The version of fastp used Freyja_FASTQ, Metabuli, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastplong_docker String Docker image used for fastplong Metabuli
fastplong_html_report File The HTML report conveying fastplong results Metabuli
fastplong_json_report File The JSON report conveying fastplong results Metabuli
fastplong_read1_trimmed File `read1` input trimmed by fastplong Metabuli
fastplong_version String The version of fastplong used Metabuli
fastq_dl_date String The date of the read data download SRA_Fetch
fastq_dl_docker String The docker used SRA_Fetch
fastq_dl_fastq_metadata File File containing metadata of the provided accession such as submission_accession, library_selection, instrument_platform, among others SRA_Fetch
fastq_dl_version String The version of fastq-dl used SRA_Fetch
fastq_dl_warning String This warning field is populated if SRA-Lite files are detected. These files contain all quality encoding as Phred-30 or Phred-3. SRA_Fetch
fastq_files Array[File] FASTQ files produced from basecalling and demultiplexing Dorado_Basecalling
fastq_scan_clean1_json File The JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length TBProfiler_tNGS, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_clean1_json String The JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length Freyja_FASTQ
fastq_scan_clean2_json File The JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length Freyja_FASTQ, TBProfiler_tNGS, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_clean_pairs String Number of read pairs after cleaning TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_docker String The Docker image of fastq_scan TBProfiler_tNGS, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_num_reads_clean1 Int The number of forward reads after cleaning as calculated by fastq_scan TBProfiler_tNGS, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_num_reads_clean1 String The number of forward reads after cleaning as calculated by fastq_scan Freyja_FASTQ
fastq_scan_num_reads_clean2 Int The number of reverse reads after cleaning as calculated by fastq_scan Freyja_FASTQ, TBProfiler_tNGS, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_num_reads_clean_pairs String The number of read pairs after cleaning as calculated by fastq_scan Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastq_scan_num_reads_raw1 Int The number of input forward reads as calculated by fastq_scan TBProfiler_tNGS, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_num_reads_raw1 String The number of input forward reads as calculated by fastq_scan Freyja_FASTQ
fastq_scan_num_reads_raw2 Int The number of input reserve reads as calculated by fastq_scan Freyja_FASTQ, TBProfiler_tNGS, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_num_reads_raw_pairs String The number of input read pairs as calculated by fastq_scan Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastq_scan_r1_mean_q_clean Float The average quality of forward reads after cleaning as calculated by fastq_scan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
fastq_scan_r1_mean_q_raw Float The average quality of forward reads as calculated by fastq_scan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
fastq_scan_r1_mean_readlength_clean Float The average read length of forward reads after cleaning as calculated by fastq_scan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
fastq_scan_r1_mean_readlength_raw Float The average read length of forward reads as calculated by fastq_scan TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
fastq_scan_r2_mean_q_clean Float The average quality of reverse reads after cleaning as calculated by fastq_scan TheiaCoV_Illumina_PE
fastq_scan_r2_mean_q_raw Float The average quality of reverse reads as calculated by fastq_scan TheiaCoV_Illumina_PE
fastq_scan_r2_mean_readlength_clean Float The average read length of reverse reads after cleaning as calculated by fastq_scan TheiaCoV_Illumina_PE
fastq_scan_r2_mean_readlength_raw Float The average read length of reverse reads as calculated by fastq_scan TheiaCoV_Illumina_PE
fastq_scan_raw1_json File The JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length TBProfiler_tNGS, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_raw1_json String The JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length Freyja_FASTQ
fastq_scan_raw2_json File The JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length Freyja_FASTQ, TBProfiler_tNGS, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_raw_pairs String Number of raw read pairs TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel
fastq_scan_version String The version of fastq_scan Freyja_FASTQ, TBProfiler_tNGS, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
fastqc_clean1_html File An HTML file that provides a graphical visualization of clean forward read quality from fastqc to open in an internet browser TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fastqc_clean1_html String An HTML file that provides a graphical visualization of clean forward read quality from fastqc to open in an internet browser Freyja_FASTQ
fastqc_clean2_html File An HTML file that provides a graphical visualization of clean reverse read quality from fastqc to open in an internet browser Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_docker String The Docker container used for fastqc Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fastqc_num_reads_clean1 Int The number of forward reads after cleaning by fastqc TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fastqc_num_reads_clean1 String The number of forward reads after cleaning by fastqc Freyja_FASTQ
fastqc_num_reads_clean2 Int The number of reverse reads after cleaning by fastqc Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_num_reads_clean_pairs String The number of read pairs after cleaning by fastqc Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_num_reads_raw1 Int The number of input forward reads by fastqc before cleaning TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fastqc_num_reads_raw1 String The number of input forward reads by fastqc before cleaning Freyja_FASTQ
fastqc_num_reads_raw2 Int The number of input reverse reads by fastqc before cleaning Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_num_reads_raw_pairs String The number of input read pairs by fastqc before cleaning Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_raw1_html File An HTML file that provides a graphical visualization of raw forward read quality from fastqc to open in an internet browser TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fastqc_raw1_html String An HTML file that provides a graphical visualization of raw forward read quality from fastqc to open in an internet browser Freyja_FASTQ
fastqc_raw2_html File An HTML file that provides a graphical visualization of raw reverse read quality from fastqc to open in an internet browser Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
fastqc_version String Version of fastqc software used Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
fetch_srr_accession_analysis_date String The date the fetch_srr_accession analysis was run. Fetch_SRR_Accession
fetch_srr_accession_version String The version of the fetch_srr_accession workflow. Fetch_SRR_Accession
file_translations File A tracking file to use for referencing original filenames and paths when identical files are indexed. Zip_Column_Content
filtered_contigs_metrics File File containing metrics of contigs filtered TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
flu_A_315675_resistance String resistance mutations to A_315675 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_amantadine_resistance String resistance mutations to amantadine TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_compound_367_resistance String resistance mutations to compound_367 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_favipiravir_resistance String resistance mutations to favipiravir TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_fludase_resistance String resistance mutations to fludase TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_L_742_001_resistance String resistance mutations to L_742_001 TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_laninamivir_resistance String resistance mutations to laninamivir TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_oseltamivir_resistance String resistance mutations to oseltamivir (Tamiflu®) TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_peramivir_resistance String resistance mutations to peramivir (Rapivab®) TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_pimodivir_resistance String resistance mutations to pimodivir TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_rimantadine_resistance String resistance mutations to rimantadine TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_xofluza_resistance String resistance mutations to xofluza (Baloxavir marboxil) TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flu_zanamivir_resistance String resistance mutations to zanamivir (Relenza®) TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
flye_assembly_info String Information file from Flye assembly TheiaEuk_ONT, TheiaProk_ONT
flye_denovo_docker String Docker image used for Flye TheiaViral_ONT
flye_denovo_info File Information file from Flye assembly TheiaViral_ONT
flye_denovo_status String Status of Flye assembly TheiaViral_ONT
flye_denovo_version String Version of Flye used TheiaViral_ONT
flye_version String Version of Flye software used TheiaEuk_ONT, TheiaProk_ONT
freyja_abundances String Abundances estimates identified by Freyja and parsed from freyja_demixed file Freyja_FASTQ
freyja_barcode_file String Barcode file used with Freyja Freyja_FASTQ
freyja_barcode_version String Name of barcode file used, or the date if update_db is true Freyja_FASTQ
freyja_bootstrap_lineages String A CSV that contains the 0.025, 0.05, 0.25, 0.5 (median), 0.75, 0.95, and 0.975 percentiles for each lineage Freyja_FASTQ
freyja_bootstrap_lineages_pdf String A boxplot of the bootstrap lineages CSV file Freyja_FASTQ
freyja_bootstrap_summary String A CSV that contains the 0.025, 0.05, 0.25, 0.5 (median), 0.75, 0.95, and 0.975 percentiles for each WHO designated VOI/VOC Freyja_FASTQ
freyja_bootstrap_summary_pdf String A boxplot of the bootstrap summary CSV file Freyja_FASTQ
freyja_coverage Float Coverage identified by Freyja and parsed from freyja_demixed file Freyja_FASTQ
freyja_dashboard File The HTML file of the dashboard created Freyja_Dashboard
freyja_dashboard_metadata File The metadata used to create the dashboard Freyja_Dashboard
freyja_dashboard_version String The version of Freyja used Freyja_Dashboard
freyja_dashboard_wf_analysis_date String The date of analysis Freyja_Dashboard
freyja_dashboard_wf_version String The version of the Public Health Bioinformatics (PHB) repository used Freyja_Dashboard
freyja_demixed File The main output TSV; see the section directly above this table for an explanation Freyja_FASTQ
freyja_demixed_aggregate File A TSV file that summarizes the `freyja_demixed` outputs for all samples Freyja_Dashboard, Freyja_Plot
freyja_demixed_parsed File Parsed freyja_demixed file, containing the same information, for easy result concatenation Freyja_FASTQ
freyja_depths File A TSV listing the depth of every position Freyja_FASTQ
freyja_fastq_wf_analysis_date String Date of analysis Freyja_FASTQ
freyja_fastq_wf_version String The version of the Public Health Bioinformatics (PHB) repository used Freyja_FASTQ
freyja_lineage_metadata_file String Metadata file for lineages identified by Freyja Freyja_FASTQ
freyja_lineages String Lineages in descending order identified by Freyja and parsed from freyja_demixed file Freyja_FASTQ
freyja_metadata_version String Name of lineage metadata file used, or the date if update_db is true Freyja_FASTQ
freyja_plot File A PDF of the plot produced by the workflow Freyja_Plot
freyja_plot_metadata File The metadata used to create the plot Freyja_Plot
freyja_plot_version String The version of Freyja used Freyja_Plot
freyja_plot_wf_analysis_date String The date of analysis Freyja_Plot
freyja_plot_wf_version String The version of the Public Health Bioinformatics (PHB) repository used Freyja_Plot
freyja_resid String Residual of the weighted least absolute deviation problem used to estimate lineage abundances identified by Freyja and parsed from freyja_demixed file Freyja_FASTQ
freyja_summarized String Sum of all lineage abundances in a particular WHO designation identified by Freyja and parsed from freyja_demixed file Freyja_FASTQ
freyja_variants File The TSV file containing the variants identified by Freyja Freyja_FASTQ
freyja_version String version of Freyja used Freyja_FASTQ
gambit_closest_genomes File CSV file listing genomes in the GAMBIT database that are most similar to the query assembly Gambit_Query, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_closest_genomes_file File CSV file listing genomes in the GAMBIT database that are most similar to the query assembly TheiaEuk_ONT
gambit_db_version String Version of the GAMBIT database used Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_docker String GAMBIT Docker used Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_next_taxon String Next taxon predicted by GAMBIT TheiaEuk_ONT
gambit_next_taxon_rank String Next taxon rank predicted by GAMBIT TheiaEuk_ONT
gambit_predicted_taxon String Taxon predicted by GAMBIT Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_predicted_taxon_rank String Taxon rank of GAMBIT taxon prediction Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_query_wf_analysis_date String Date of analysis Gambit_Query
gambit_query_wf_version String PHB repository version Gambit_Query
gambit_report File GAMBIT report in a machine-readable format Gambit_Query, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gambit_report_file File GAMBIT report in a machine-readable format TheiaEuk_ONT
gambit_version String Version of GAMBIT software used Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma_docker String The Docker container used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma_fasta File The FASTA file reporting gene matches if boolean was set to true TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma_gff File The GFF file reporting gene matches if boolean was set to true TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma_results File The .gamma file reporting gene matches TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gamma_version String The version of GAMMA used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genbank_fasta File **Only for SARS-CoV-2 submission**: GenBank fasta file for upload Mercury_Prep_N_Batch
genbank_metadata File **Only for SARS-CoV-2 submission**: GenBank metadata for upload Mercury_Prep_N_Batch
generated_accessions File Text file mapping the BioSample accession with its sample name. Terra_2_NCBI
genoflu_all_segments String The genotypes for each individual flu segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
genoflu_genotype String The genotype of the whole genome, based off of the individual segments types TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
genoflu_output_tsv File The output file from GenoFLU TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
genoflu_version String The version of GenoFLU used TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
genotyphi_final_genotype String Final genotype call from GenoTyphi TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_genotype_confidence String Confidence in the final genotype call made by GenoTyphi TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_mykrobe_json File JSON file of GenoTyphi output, described <https://github.com/katholt/genotyphi#explanation-of-columns-in-the-output> TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_report_tsv File TSV file of GenoTyphi output, described <https://github.com/katholt/genotyphi#explanation-of-columns-in-the-output> TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_species String Species call from Mykrobe, used to run GenoTyphi TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_st_probes_percent_coverage Float Percentage coverage to the Typhi MLST probes TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
genotyphi_version String Version of GenoTyphi used TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
gisaid_cli_version String The verison of the GISAID CLI tool Terra_2_GISAID
gisaid_fasta File **Only for mpox and SARS-CoV-2 submission**: GISAID fasta file for upload Mercury_Prep_N_Batch
gisaid_logs File The log files regarding the submission Terra_2_GISAID
gisaid_metadata File **Only for mpox and SARS-CoV-2 submission**: GISAID metadata for upload Mercury_Prep_N_Batch
hicap_docker String Docker image used for hicap TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
hicap_genes String cap genes identified. genes on different contigs delimited by;. truncation shown by trailing * TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
hicap_results_tsv File TSV file of hicap output TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
hicap_serotype String hicap serotype TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
hicap_version String hicap version used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
identified_organisms Array[String] List of organisms extracted and identified from an panel level sample TheiaViral_Panel
irma_aligned_fastqs File Reads aligned to Flu reference from IRMA TheiaViral_ONT
irma_all_deletions_tsv File Concatenated TSV file of all deletions identified by IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_all_insertions_tsv File Concatenated TSV file of all insertions identified by IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_all_snvs_tsv File Concatenated TSV file of all SNVs identified by IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_assembly_fasta_concatenated File Assembly FASTA file of all Influenza genome segments concatenated into one sequence/FASTA entry TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_bams Array[File] Aligned reads from IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_docker String Docker image used to run IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
irma_ha_segment_fasta File HA (Haemagglutinin) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_min_consensus_support_threshold Int Minimum consensus support threshold used by IRMA with ONT data. For illumina data, see output called `consensus_n_variant_min_depth` for this value TheiaCoV_ONT
irma_mp_segment_fasta File MP (Matrix Protein) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_na_segment_fasta File NA (Neuraminidase) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_np_segment_fasta File NP (Nucleoprotein) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_ns_segment_fasta File NS (Nonstructural) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_pa_segment_fasta File PA (Polymerase acidic) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_pb1_segment_fasta File PB1 (Polymerase basic 1) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_pb2_segment_fasta File PB2 (Polymerase basic 2) assembly fasta file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_qc_log File IRMA QC log file TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_qc_summary_tsv File TSV file summarizing IRMA quality control metrics TheiaCoV_Illumina_PE, TheiaCoV_ONT
irma_read1_aligned File Read1 aligned to Flu reference from IRMA TheiaViral_Illumina_PE
irma_read2_aligned File Read2 aligned to Flu reference from IRMA TheiaViral_Illumina_PE
irma_subtype String Flu subtype as determined by IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
irma_subtype_notes String Helpful note to user about Flu B subtypes. Output will be blank for Flu A samples. For Flu B samples it will state: "IRMA does not differentiate Victoria and Yamagata Flu B lineages. See abricate_flu_subtype output column" TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
irma_type String Flu type as determined by IRMA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
irma_version String Version of IRMA used TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
ivar_tsv File Variant descriptor file generated by iVar variants TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
ivar_variant_proportion_intermediate String The proportion of variants of intermediate frequency TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
ivar_variant_version String Version of iVar for running the iVar variants command TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
ivar_vcf File iVar tsv output converted to VCF format TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
ivar_version_consensus String Version of iVar for running the iVar consensus command TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaViral_Illumina_PE
ivar_version_primtrim String Version of iVar for running the iVar trim command Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kaptive_k_locus String Best matching K locus identified by Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_k_type String Best matching K type identified by Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_kl_confidence String Kaptive’s confidence in the KL match (see <https://github.com/katholt/Kaptive/wiki/Interpreting-the-results>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_oc_locus String Best matching K locus identified by Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_ocl_confidence String Kaptive’s confidence in the OCL match (see <https://github.com/katholt/Kaptive/wiki/Interpreting-the-results>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_output_file_k File TSV <https://github.com/katholt/Kaptive/wiki/How-to-run#output-filesfrom> the K locus from Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_output_file_oc File TSV <https://github.com/katholt/Kaptive/wiki/How-to-run#output-filesfrom> the OC locus from Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kaptive_version String Version of Kaptive used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_docker String Kleborate docker image used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_genomic_resistance_mutations String Genomic resistance mutations identifies by Kleborate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_key_resistance_genes String Key resistance genes identified by Kleborate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_klocus String Best matching K locus identified by Kleborate via Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_klocus_confidence String Kaptive’s confidence in the KL match (see <https://github.com/katholt/Kaptive/wiki/Interpreting-the-results>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_ktype String Best matching K type identified by Kleborate via Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_mlst_sequence_type String <https://github.com/katholt/Kleborate/wiki/MLST#multi-locus-sequence-typing-mlst> call by Kleborate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_olocus String Best matching OC locus identified by Kleborate via Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_olocus_confidence String Kaptive’s confidence in the KL match (see <https://github.com/katholt/Kaptive/wiki/Interpreting-the-results>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_otype String Best matching OC type identified by Kleborate via Kaptive TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_output_file File See also <https://github.com/katholt/Kleborate/wiki/Scores-and-counts> TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_resistance_score String Resistance score as given by kleborate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_version String Version of Kleborate used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kleborate_virulence_score String Virulence score as given by kleborate TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_database String Database used to run KmerFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_docker String Docker image used to run KmerFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_query_coverage String KmerFinder’s query coverage of the top hit result TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_results_tsv File Output TSV file created by KmerFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_template_coverage String Percent of kmer coverage pertaining to the template, or reference selected TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kmerfinder_top_hit String Top hit species of KmerFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
kraken2_classified_read1 File FASTQ file of classified forward/R1 reads Kraken_PE, Kraken_SE
kraken2_classified_read2 File FASTQ file of classified reverse/R2 reads (if PE) Kraken_PE
kraken2_classified_report File Standard Kraken2 output report. TXT filetype, but can be opened in Excel as a TSV file Kraken_PE, Kraken_SE, TheiaViral_Panel
kraken2_database String Kraken2 database used for the taxonomic assignment TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
kraken2_docker String Docker image used to run kraken2 Kraken_PE, Kraken_SE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
kraken2_extracted_read1 File Forward reads extracted by taxonomic classification TheiaViral_Illumina_PE
kraken2_extracted_read2 File Reverse reads extracted by taxonomic classification TheiaViral_Illumina_PE
kraken2_extraction_status String "PASS"/"FAIL" depending on if reads could be extracted TheiaViral_Illumina_PE
kraken2_pe_wf_analysis_date String Date the workflow was run Kraken_PE
kraken2_pe_wf_version String Workflow version Kraken_PE
kraken2_percent_human_clean Float The percentage of human-classified reads in the sample's clean reads TheiaMeta_Illumina_PE, TheiaViral_Panel
kraken2_percent_human_raw Float The percentage of human-classified reads in the sample's raw reads TheiaMeta_Illumina_PE, TheiaViral_Panel
kraken2_report String TXT document describing taxonomic prediction of every FASTQ record. This file is usually very large and cumbersome to open and view TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE
kraken2_report File TXT document describing taxonomic prediction of every FASTQ record. This file is usually very large and cumbersome to open and view Kraken_PE, Kraken_SE
kraken2_report_clean File The full Kraken report for the sample's clean reads TheiaMeta_Illumina_PE, TheiaViral_Panel
kraken2_report_raw File The full Kraken report for the sample's raw reads TheiaMeta_Illumina_PE, TheiaViral_Panel
kraken2_se_wf_analysis_date String Date the workflow was run Kraken_SE
kraken2_se_wf_version String Workflow version Kraken_SE
kraken2_unclassified_read1 File FASTQ file of unclassified forward/R1 reads Kraken_PE, Kraken_SE
kraken2_unclassified_read2 File FASTQ file of unclassified reverse/R2 reads (if PE) Kraken_PE
kraken2_version String The version of kraken2 used Kraken_PE, Kraken_SE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaViral_Illumina_PE, TheiaViral_Panel
kraken_docker String Docker image used for Kraken TheiaProk_Illumina_PE
kraken_human Float Percent of human read data detected using the Kraken2 software TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_human String Percent of human read data detected using the Kraken2 software Freyja_FASTQ
kraken_human_dehosted Float Percent of human read data detected using the Kraken2 software after host removal NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_human_dehosted String Percent of human read data detected using the Kraken2 software after host removal Freyja_FASTQ
kraken_report File Full Kraken report TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_report String Full Kraken report Freyja_FASTQ
kraken_report_dehosted File Full Kraken report after host removal NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_report_dehosted String Full Kraken report after host removal Freyja_FASTQ
kraken_target_organism String Percent of target organism read data detected using the Kraken2 software TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_target_organism_dehosted String Percent of target organism read data detected using the Kraken2 software after host removal NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_target_organism_name String The name of the target organism; e.g., "Monkeypox" or "Human immunodeficiency virus" TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_version String Version of Kraken software used Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
kraken_version_dehosted String Version of Kraken2 software used NCBI_Scrub_PE, NCBI_Scrub_SE
krona_docker String The docker image of Krona Kraken_PE, Kraken_SE, TheiaMeta_Illumina_PE
krona_html File HTML report of krona with visualisation of taxonomic classification of reads (if PE or SE) Kraken_PE, Kraken_SE
krona_html_clean File The KronaPlot after reads are cleaned TheiaMeta_Illumina_PE
krona_html_raw File The KronaPlot before reads are cleaned TheiaMeta_Illumina_PE
krona_version String The version of Krona Kraken_PE, Kraken_SE, TheiaMeta_Illumina_PE
ksnp3_core_snp_matrix File The SNP matrix made with the core genome; formatted for Phandango if `phandango_coloring` input is `true` kSNP3
ksnp3_core_snp_matrix_status String Will print either `The core SNP matrix was produced` OR `The core SNP matrix could not be produced` kSNP3
ksnp3_core_snp_table File Formatted version of ksnp3_vcf_ref_genome file with only core SNPs, sorted by number of occurrences in the sample set kSNP3
ksnp3_core_tree File The phylogenetic tree made with the core genome kSNP3
ksnp3_docker String The docker image used kSNP3
ksnp3_filtered_metadata File Optional output file with filtered metadata that is only produced if the optional `summarize_data` task is used. kSNP3
ksnp3_ml_tree File Maximum likelihood tree that is only produced if `ksnp3_args` includes `"-ML"` kSNP3
ksnp3_nj_tree File Neighbor joining tree that is only produced if `ksnp3_args` includes `"-NJ"` kSNP3
ksnp3_number_core_snps String Number of core SNPs in the sample set kSNP3
ksnp3_number_snps String Number of SNPs in the sample set kSNP3
ksnp3_pan_snp_matrix File The SNP matrix made with the pangenome; formatted for Phandango if `phandango_coloring` input is `true` kSNP3
ksnp3_pan_tree File The phylogenetic tree made with the pangenome kSNP3
ksnp3_snp_dists_version String The version of snp_dists used in the workflow kSNP3
ksnp3_snps File File containing the set of SNPs used in the analysis. Required if more trees are to be appended to the existing one. kSNP3
ksnp3_summarized_data File CSV presence/absence matrix generated by the `summarize_data` task from the list of columns provided; formatted for Phandango if `phandango_coloring` input is `true` kSNP3
ksnp3_vcf_ref_genome File A VCF file containing the variants detected in the core genome kSNP3
ksnp3_vcf_ref_samplename String The name of the (user-supplied) sample used as the reference for calling SNPs. kSNP3
ksnp3_vcf_snps_not_in_ref File A TSV file of the SNPs not present in the reference genome, but were identified by kSNP3. kSNP3
ksnp3_wf_analysis_date String The date the workflow was run kSNP3
ksnp3_wf_version String The version of the repository the workflow is hosted in kSNP3
ksnp4_core_snp_matrix File The SNP matrix made with the core genome; formatted for Phandango if `phandango_coloring` input is `true` kSNP4
ksnp4_core_snp_matrix_status String Will print either `The core SNP matrix was produced` OR `The core SNP matrix could not be produced` kSNP4
ksnp4_core_snp_table File Formatted version of ksnp4_vcf_ref_genome file with only core SNPs, sorted by number of occurrences in the sample set kSNP4
ksnp4_core_tree File The phylogenetic tree made with the core genome kSNP4
ksnp4_docker String The docker image used kSNP4
ksnp4_filtered_metadata File Optional output file with filtered metadata that is only produced if the optional `summarize_data` task is used. kSNP4
ksnp4_ml_tree File Maximum likelihood tree that is only produced if `ksnp4_args` includes `"-ML"` kSNP4
ksnp4_nj_tree File Neighbor joining tree that is only produced if `ksnp4_args` includes `"-NJ"` kSNP4
ksnp4_number_core_snps String Number of core SNPs in the sample set kSNP4
ksnp4_number_snps String Number of SNPs in the sample set kSNP4
ksnp4_pan_snp_matrix File The SNP matrix made with the pangenome; formatted for Phandango if `phandango_coloring` input is `true` kSNP4
ksnp4_pan_tree File The phylogenetic tree made with the pangenome kSNP4
ksnp4_snp_dists_version String The version of snp_dists used in the workflow kSNP4
ksnp4_snps File File containing the set of SNPs used in the analysis. Required if more trees are to be appended to the existing one. kSNP4
ksnp4_summarized_data File CSV presence/absence matrix generated by the `summarize_data` task from the list of columns provided; formatted for Phandango if `phandango_coloring` input is `true` kSNP4
ksnp4_vcf_ref_genome File A VCF file containing the variants detected in the core genome kSNP4
ksnp4_vcf_ref_samplename String The name of the (user-supplied) sample used as the reference for calling SNPs. kSNP4
ksnp4_vcf_snps_not_in_ref File A TSV file of the SNPs not present in the reference genome, but were identified by kSNP4. kSNP4
ksnp4_wf_analysis_date String The date the workflow was run kSNP4
ksnp4_wf_version String The version of the repository the workflow is hosted in kSNP4
largest_contig Int The size of the largest contig in basepairs TheiaMeta_Illumina_PE
legsta_predicted_sbt String Sequence based type predicted by Legsta TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
legsta_results File TSV file of legsta results (see <https://github.com/tseemann/legsta#output>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
legsta_version String Version of legsta used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
lissero_results File TSV results file from LisSero (see <https://github.com/MDU-PHL/LisSero#example-output>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
lissero_serotype String Serotype predicted by LisSero TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
lissero_version String Version of LisSero used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
lyveset_alignment_fasta File The output alignment file in fasta format Lyve_SET
lyveset_docker_image String Lyve_SET docker image used for analysis Lyve_SET
lyveset_log File Lyve_SET task log file Lyve_SET
lyveset_pairwise_matrix File Pairwise SNP distances matrix Lyve_SET
lyveset_pooled_snps_vcf File SNPs vcf Lyve_SET
lyveset_raxml_tree File RAxML-generated tree in newick format Lyve_SET
lyveset_wf_analysis_date String Date analysis was run Lyve_SET
lyveset_wf_version String Version of PHB used when running Lyveset_PHB Lyve_SET
mashtree_docker String The Docker image used to run the mashtree task MashTree_FASTA
mashtree_filtered_metadata File Optional output file with filtered metadata that is only produced if the optional `summarize_data` task is used MashTree_FASTA
mashtree_matrix File The distance matrix made MashTree_FASTA
mashtree_summarized_data File CSV presence/absence matrix generated by the `summarize_data` task from the list of columns provided; formatted for Phandango if `phandango_coloring` input is `true` MashTree_FASTA
mashtree_tree File The phylogenetic tree made MashTree_FASTA
mashtree_version String The version of mashtree used in the workflow MashTree_FASTA
mashtree_wf_analysis_date String The date the workflow was run MashTree_FASTA
mashtree_wf_version String The version of PHB the workflow is hosted in MashTree_FASTA
mask_low_coverage_all_coverage_bed File BED file showing all coverage regions TheiaViral_ONT
mask_low_coverage_bed File BED file showing masked low coverage regions TheiaViral_ONT
mask_low_coverage_bedtools_docker String Docker image used for bedtools in masking TheiaViral_ONT
mask_low_coverage_bedtools_version String Version of bedtools used in masking TheiaViral_ONT
mask_low_coverage_reference_fasta File Reference FASTA with low coverage regions masked TheiaViral_ONT
meanbaseq_trim String Mean quality of the nucleotide basecalls aligned to the reference genome after primer trimming TheiaCoV_Illumina_PE
meanbaseq_trim Float Mean quality of the nucleotide basecalls aligned to the reference genome after primer trimming TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, TheiaCoV_ONT
meanmapq_trim String Mean quality of the mapped reads to the reference genome after primer trimming TheiaCoV_Illumina_PE
meanmapq_trim Float Mean quality of the mapped reads to the reference genome after primer trimming TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, TheiaCoV_ONT
medaka_model String Model used by Medaka TheiaEuk_ONT, TheiaProk_ONT
medaka_reference String Reference sequence used in medaka task TheiaCoV_ClearLabs, TheiaCoV_ONT
medaka_vcf File A VCF file containing the identified variants TheiaCoV_ONT
medaka_version String Version of Medaka used TheiaEuk_ONT, TheiaProk_ONT
megahit_docker String Docker image used for MEGAHIT TheiaViral_Illumina_PE
megahit_status String Status of the MEGAHIT assembly TheiaViral_Illumina_PE
megahit_version String Version of MEGAHIT used TheiaViral_Illumina_PE
meningotype_BAST String BAST type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_FetA String FetA type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_fHbp String fHbp type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_NadA String NBA type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_NHBA String NHBA type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_PorA String PorA type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_PorB String PorB type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_serogroup String Serogroup TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_tsv File Full result file TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
meningotype_version String Version of meningotype used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
mercury_prep_n_batch_analysis_date String Date analysis was run Mercury_Prep_N_Batch
mercury_prep_n_batch_version String Version of the PHB repository that hosts this workflow Mercury_Prep_N_Batch
mercury_script_version String Version of the Mercury tool that was used in this workflow Mercury_Prep_N_Batch
merlin_tag String Merlin tag for the assembly TheiaEuk_ONT
metabuli_classified File Classified reads from Metabuli TheiaViral_ONT
metabuli_classified_read1 File FASTQ of `read1` input classified by Metabuli Metabuli
metabuli_classified_read2 File FASTQ of `read2` input classified by Metabuli Metabuli
metabuli_classified_report File Classification report from Metabuli Metabuli
metabuli_database String Database used for Metabuli TheiaProk_ONT, TheiaViral_ONT
metabuli_docker String Docker image used for Metabuli Metabuli, TheiaProk_ONT, TheiaViral_ONT
metabuli_human Float Percent of human reads detected in raw reads Freyja_FASTQ, TheiaCoV_ONT
metabuli_human_dehosted Float Percent of human reads detected after removing human reads Freyja_FASTQ, TheiaCoV_ONT
metabuli_krona_report File Krona visualization report from Metabuli Metabuli, TheiaViral_ONT
metabuli_percent_target_lineage String Percent of reads classified to the target lineage TheiaViral_ONT
metabuli_read1_extract File Extracted reads from Metabuli TheiaViral_ONT
metabuli_report String Classification report from Metabuli Freyja_FASTQ, TheiaCoV_ONT, TheiaProk_ONT
metabuli_report File Classification report from Metabuli Metabuli, TheiaViral_ONT
metabuli_report_dehosted String Classification report from Metabuli after removing human reads Freyja_FASTQ, TheiaCoV_ONT
metabuli_status String Status of Metabuli analysis Metabuli, TheiaViral_ONT
metabuli_target_organism String Percent of reads classified to target organism for Metabuli analysis TheiaCoV_ONT
metabuli_target_organism_dehosted String Percent of reads classified to target organism for Metabuli analysis after removing human reads TheiaCoV_ONT
metabuli_target_organism_name String Name of the target organism for Metabuli analysis TheiaCoV_ONT
metabuli_version String Version of Metabuli used Freyja_FASTQ, Metabuli, TheiaCoV_ONT, TheiaProk_ONT, TheiaViral_ONT
metabuli_wf_analysis_date String Analysis date for Metabuli workflow Metabuli
metabuli_wf_version String Version of Metabuli workflow Metabuli
metaspades_docker String The Docker image of metaspades TheiaMeta_Illumina_PE
metaspades_version String The version of metaspades TheiaMeta_Illumina_PE
metaviralspades_docker String Docker image used for MetaviralSPAdes TheiaViral_Illumina_PE
metaviralspades_status String Status of MetaviralSPAdes assembly TheiaViral_Illumina_PE
metaviralspades_version String Version of MetaviralSPAdes used TheiaViral_Illumina_PE
microreact_api_response File Result of the Microreact API request Microreact_Export
microreact_input File A project file in JSON format that can be used for manual upload to Microreact Microreact_Export
midas_docker String MIDAS docker image used TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
midas_primary_genus String The primary genus detected by MIDAS TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
midas_report File TSV report of full MIDAS results TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
midas_secondary_genus String Genus of the next most abundant species after removing all species of the most abundant genus TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
midas_secondary_genus_abundance Float Relative abundance of secondary genus TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
midas_secondary_genus_coverage Float Absolute coverage of secondary genus TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
minimap2_docker String The Docker image of minimap2 Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_ONT
minimap2_out File Output file from Minimap2 alignment TheiaViral_ONT
minimap2_version String The version of minimap2 Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_ONT
morgana_magic_organism String Standardized organism name used for characterization TheiaViral_Illumina_PE, TheiaViral_ONT
n50_value Int N50 of assembly calculated by QUAST TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
nanoplot_docker String Docker image for nanoplot TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT
nanoplot_html_clean File An HTML report describing the clean reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_html_raw File An HTML report describing the raw reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_num_reads_clean1 Int Number of clean reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_num_reads_raw1 Int Number of raw reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_est_coverage_clean Float Estimated coverage on the clean reads by nanoplot Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT
nanoplot_r1_est_coverage_raw Float Estimated coverage on the raw reads by nanoplot Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT
nanoplot_r1_mean_q_clean Float Mean quality score of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_mean_q_raw Float Mean quality score of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_mean_readlength_clean Float Mean read length of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_mean_readlength_raw Float Mean read length of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_median_q_clean Float Median quality score of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_median_q_raw Float Median quality score of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_median_readlength_clean Float Median read length of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_median_readlength_raw Float Median read length of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_n50_clean Float N50 of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_n50_raw Float N50 of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_stdev_readlength_clean Float Standard deviation read length of clean forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_r1_stdev_readlength_raw Float Standard deviation read length of raw forward reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_tsv_clean File A TSV report describing the clean reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_tsv_raw File A TSV report describing the raw reads Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
nanoplot_version String Version of nanoplot used for analysis TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT
nanoq_filtered_read1 File Filtered reads from NanoQ TheiaViral_ONT
nanoq_version String Version of nanoq used in analysis Freyja_FASTQ, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
ncbi_read_extraction_rank String Read extraction rank used Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT
ncbi_scrub_docker String The Docker image for NCBI's HRRT (human read removal tool) NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
ncbi_scrub_human_spots_removed Int Number of spots removed (or masked) NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
ncbi_scrub_pe_analysis_date String Date of analysis NCBI_Scrub_PE
ncbi_scrub_pe_version String Version of HRRT software used NCBI_Scrub_PE
ncbi_scrub_read1_dehosted File Dehosted reads after NCBI scrub TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
ncbi_scrub_read2_dehosted File Dehosted reads after NCBI scrub TheiaViral_Illumina_PE, TheiaViral_Panel
ncbi_scrub_se_analysis_date String Date of analysis NCBI_Scrub_SE
ncbi_scrub_se_version String Version of HRRT software used NCBI_Scrub_SE
ncbi_taxon_id String NCBI taxonomy ID of inputted organism following rank extraction Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT
ncbi_taxon_name String NCBI taxonomy name of inputted taxon following rank extraction Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_dels String Amino-acid deletions as detected by NextClade. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_dels_flu_h5n1 String Amino-acid deletions as detected by NextClade. Specific to flu; it includes deletions for H5N1 whole genome TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_aa_dels_flu_ha String Amino-acid deletions as detected by NextClade. Specific to flu; it includes deletions for HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_dels_flu_na String Amino-acid deletions as detected by NextClade. Specific to Flu; it includes deletions for NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_dels_rabies String Amino-acid deletions as detected by Nextclade. Specific to Monkeypox TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_subs String Amino-acid substitutions as detected by Nextclade. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_subs_flu_h5n1 String Amino-acid substitutions as detected by Nextclade. Specific to Flu; it includes substitutions for H5N1 whole genome TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_aa_subs_flu_ha String Amino-acid substitutions as detected by Nextclade. Specific to Flu; it includes substitutions for HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_subs_flu_na String Amino-acid substitutions as detected by Nextclade. Specific to Flu; it includes substitutions for NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_aa_subs_rabies String Amino-acid substitutions as detected by Nextclade. Specific to Monkeypox TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_batch_analysis_date String Date of analysis Nextclade_Batch
nextclade_batch_auspice_json File Phylogenetic tree with user placed samples Nextclade_Batch
nextclade_batch_nextclade_docker String Nextclade docker image used Nextclade_Batch
nextclade_batch_nextclade_json File JSON file with the results of the Nextclade analysis Nextclade_Batch
nextclade_batch_nextclade_tsv File Tab-delimited file with Nextclade results Nextclade_Batch
nextclade_batch_nextclade_version String Nextclade version used Nextclade_Batch
nextclade_batch_version String Version of the Public Health Bioinformatics (PHB) repository used Nextclade_Batch
nextclade_clade String Nextclade clade designation, will be blank for Flu. TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_clade_flu_h5n1 String Nextclade clade designation, specific to Flu 5N1 whole genome. NOTE: Output will be blank or `NA` since this nextclade dataset does assign clades TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_clade_flu_ha String Nextclade clade designation, specific to Flu NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_clade_flu_na String Nextclade clade designation, specific to Flu HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_clade_rabies String Nextclade clade designation, specific to Rabies TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_docker String Docker image used to run Nextclade TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_ds_tag String Dataset tag used to run Nextclade. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_ds_tag_flu_ha String Dataset tag used to run Nextclade, specific to Flu HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_ds_tag_flu_na String Dataset tag used to run Nextclade, specific to Flu NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_json File Nextclade output in JSON file format. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_json_flu_h5n1 File Nextclade output in JSON file format, specific to Flu H5N1 whole genome TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_json_flu_ha File Nextclade output in JSON file format, specific to Flu HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_json_flu_na File Nextclade output in JSON file format, specific to Flu NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_json_rabies File Nextclade output in JSON file format, specific to Rabies TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_lineage String Nextclade lineage designation TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_lineage_rabies String Nextclade lineage designation, specific to Rabies TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_qc String QC metric as determined by Nextclade. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_qc_flu_h5n1 String QC metric as determined by Nextclade, specific to Flu H5N1 whole genome TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_qc_flu_ha String QC metric as determined by Nextclade, specific to Flu HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_qc_flu_na String QC metric as determined by Nextclade, specific to Flu NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_qc_rabies String QC metric as determined by Nextclade, specific to Rabies TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_tsv File Nextclade output in TSV file format. Will be blank for Flu TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_tsv_flu_h5n1 File Nextclade output in TSV file format, specific to Flu H5N1 whole genome TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT
nextclade_tsv_flu_ha File Nextclade output in TSV file format, specific to Flu HA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_tsv_flu_na File Nextclade output in TSV file format, specific to Flu NA segment TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_tsv_rabies File Nextclade output in TSV file format, specific to Rabies TheiaViral_Illumina_PE, TheiaViral_ONT
nextclade_version String The version of Nextclade software used TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
ngmaster_ngmast_porB_allele String porB allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngmast_sequence_type String NG-MAST sequence type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngmast_tbpB_allele String tbpB allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_23S_allele String 23S rRNA allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_gyrA_allele String gyrA allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_mtrR_allele String mtrR allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_parC_allele String parC allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_penA_allele String penA allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_ponA_allele String ponA allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_porB_allele String porB allele number TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_ngstar_sequence_type String NG-STAR sequence type TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_tsv File TSV file with NG-MAST/NG-STAR typing TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
ngmaster_version String ngmaster version TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
number_contigs Int Total number of contigs in assembly TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
number_Degenerate Int Number of degenerate basecalls within the consensus assembly TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
number_N Int Number of fully ambiguous basecalls within the consensus assembly TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
number_Total Int Total number of nucleotides within the consensus assembly TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
pango_lineage String Pango lineage as determined by Pangolin Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pango_lineage_expanded String Pango lineage without use of aliases; e.g., "BA.1" → "B.1.1.529.1" Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pango_lineage_log File TSV file listing Pangolin lineage assignments and software versions for this sample Pangolin_Update
pango_lineage_report File Full Pango lineage report generated by Pangolin Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pangolin_assignment_version String The version of the pangolin software (e.g. PANGO or PUSHER) used for lineage assignment Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pangolin_conflicts String Number of lineage conflicts as determined by Pangolin Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pangolin_docker String Docker image used to run Pangolin Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pangolin_notes String Lineage notes as determined by Pangolin Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
pangolin_update_analysis_date String Date of analysis Pangolin_Update
pangolin_update_version String Version of the Public Health Bioinformatics (PHB) repository used Pangolin_Update
pangolin_updates String Result of Pangolin Update (lineage changed versus unchanged) with lineage assignment and date of analysis Pangolin_Update
pangolin_versions String All Pangolin software and database versions Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
parse_mapping_samtools_docker String Docker image used for samtools in parse mapping TheiaViral_ONT
parse_mapping_samtools_version String Version of samtools used in parse mapping TheiaViral_ONT
pasty_all_serogroups File TSV file with details of each serogroup from pasty (see <https://github.com/rpetit3/pasty#example-prefixdetailstsv>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_blast_hits File TSV file of BLAST hits from pasty (see <https://github.com/rpetit3/pasty#example-prefixblastntsv>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_comment String TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_docker String pasty docker image used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_serogroup String Serogroup predicted by pasty TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_serogroup_coverage Float The breadth of coverage of the O-antigen by pasty TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_serogroup_fragments Int Number of BLAST hits included in the prediction (fewer is better) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_summary_tsv File TSV summary file of pasty outputs (see <https://github.com/rpetit3/pasty#example-prefixtsv>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pasty_version String Version of pasty used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pbptyper_docker String pbptyper docker image used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pbptyper_pbptype_predicted_tsv File TSV file of pbptyper results (see <https://github.com/rpetit3/pbptyper#example-prefixtsv>) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pbptyper_predicted_1A_2B_2X String PBP type predicted by pbptyper TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
pbptyper_version String Version of pbptyper used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
percent_coverage Float The percentage coverage of the reference genome provided if one was provided TheiaMeta_Illumina_PE
percent_reference_coverage Float Percent coverage of the reference genome after performing primer trimming; calculated as assembly_length_unambiguous / length of the reference genome (SC2: 29903) x 100 TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
percentage_mapped_reads String Percentage of clean reads that successfully aligned to the reference genome. This value is calculated by number of mapped reads / total number of reads x 100. TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
percentage_mapped_reads Float Percentage of clean reads that successfully aligned to the reference genome. This value is calculated by number of mapped reads / total number of reads x 100. TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE
phylocompare_phb_version String The version of the Public Health Bioinformatics (PHB) repository used PhyloCompare
phylovalidate_distance String The quantitative distance between two phylogenies' tip/branch arrangements PhyloCompare
phylovalidate_flag String Flag depicting potential confounding factors during validation status PhyloCompare
phylovalidate_report File Report file summarizing the validation results PhyloCompare
phylovalidate_tree1_clean File Cleaned version of the first phylogenetic tree PhyloCompare
phylovalidate_tree2_clean File Cleaned version of the second phylogenetic tree PhyloCompare
phylovalidate_version String Version of phylovalidate used PhyloCompare
pilon_docker String The Docker image for pilon TheiaMeta_Illumina_PE
pilon_version String The version of pilon TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
pirate_core_alignment_fasta File Nucleotide alignments of the core genes as created using MAFFT within Pirate. Loci are ordered according to the gene_families.ordered file. Core_Gene_SNP
pirate_core_alignment_gff File Annotation data for the gene family within the corresponding fasta file Core_Gene_SNP
pirate_core_snp_matrix File SNP distance matrix created from the core gene alignment Core_Gene_SNP
pirate_docker_image String Pirate docker image used Core_Gene_SNP
pirate_filtered_metadata File Filtered metadata for the core gene alignment Core_Gene_SNP
pirate_gene_families_ordered File Summary of all gene families, as estimated by Pirate Core_Gene_SNP
pirate_iqtree_core_tree File Phylogenetic tree produced by IQ-TREE from the core gene alignment Core_Gene_SNP
pirate_iqtree_pan_tree File Phylogenetic tree produced by IQ-TREE from the pangenome alignment Core_Gene_SNP
pirate_iqtree_version String IQ-TREE version used Core_Gene_SNP
pirate_pan_alignment_fasta File Nucleotide alignments of the pangenome by gene as created using MAFFT within Pirate. Loci are ordered according to the gene_families.ordered file. Core_Gene_SNP
pirate_pan_alignment_gff File Annotation data for the gene family within the corresponding fasta file Core_Gene_SNP
pirate_pan_snp_matrix File SNP distance matrix created from the pangenome alignment Core_Gene_SNP
pirate_pangenome_summary File Summary of the number and frequency of genes in the pangenome, as estimated by Pirate Core_Gene_SNP
pirate_presence_absence_csv File A file generated by Pirate that allows many post-alignment tools created for Roary to be used on the output from Pirate Core_Gene_SNP
pirate_snps_dists_version String Version of snp-dists used Core_Gene_SNP
pirate_summarized_data File The presence/absence matrix generated by the summarize_data task from the list of columns provided Core_Gene_SNP
plasmidfinder_db_version String Version of PlasmidFnder used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
plasmidfinder_docker String PlasmidFinder docker image used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
plasmidfinder_plasmids String Names of plasmids identified by PlasmidFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
plasmidfinder_results File Output file from PlasmidFinder in TSV format TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
plasmidfinder_seqs File Hit_in_genome_seq.fsa file produced by PlasmidFinder TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
polypolish_version String Version of Polypolish used TheiaEuk_ONT, TheiaProk_ONT
poppunk_docker String PopPUNK docker image with GPSC database used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
poppunk_gps_cluster String GPS cluster predicted by PopPUNK TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
poppunk_GPS_db_version String Version of GPSC database used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
poppunk_gps_external_cluster_csv File GPSC v6 scheme designations TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
poppunk_version String Version of PopPUNK used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
porechop_trimmed_read1 File Trimmed reads from Porechop TheiaViral_ONT
porechop_version String Version of Porechop used TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT
prepped_ena_data File Prepared data formatted for ENA submission Terra_2_ENA
primer_bed_name String Name of the primer bed files used for primer trimming Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
primer_trimmed_read_percent Float Percentage of read data with primers trimmed as determined by iVar trim Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
prokka_gbk File GenBank file produced from Prokka annotation of input FASTA TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
prokka_gff File Prokka output GFF3 file containing sequence and annotation (you can view this in IGV) TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
prokka_sqn File A Sequin file for GenBank submission TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
qc_check String A string that indicates whether or not the sample passes a set of pre-determined and user-provided QC thresholds Freyja_FASTQ, 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
qc_standard File The file used in the QC Check task containing the QC thresholds. Freyja_FASTQ, 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
qualimap_coverage_plots_html File Interactive HTML Plots of Coverage Across the Genome Freyja_FASTQ
qualimap_docker String Qualimap docker image used Freyja_FASTQ
qualimap_reports_bundle File Zipped bundle of Qualimap reports and plots Freyja_FASTQ
qualimap_version String Version of Qualimap used Freyja_FASTQ
quasitools_coverage_file File The coverage report created by Quasitools HyDRA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quasitools_date String Date of Quasitools analysis TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quasitools_dr_report File Drug resistance report created by Quasitools HyDRA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quasitools_hydra_vcf File The VCF created by Quasitools HyDRA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quasitools_mutations_report File The mutation report created by Quasitools HyDRA TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quasitools_version String Version of Quasitools used TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_docker String Docker image used for QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_gc_percent Float GC percentage of de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_genome_length Int Genome length of de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_largest_contig Int Size of largest contig in de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_n50_value Int N50 value of de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_number_contigs Int Number of contigs in de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_report File QUAST report for de novo assembly TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_uncalled_bases Float Number of uncalled bases in de novo assembly from QUAST TheiaViral_Illumina_PE, TheiaViral_ONT
quast_denovo_version String Version of QUAST used TheiaViral_Illumina_PE, TheiaViral_ONT
quast_docker String The Docker image of QUAST TheiaMeta_Illumina_PE
quast_gc_percent Float The GC percent of your sample TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
quast_report File TSV report from QUAST TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
quast_version String The version of QUAST TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
r1_mean_q_clean Float Mean quality score of clean forward reads TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
r1_mean_q_raw Float Mean quality score of raw forward reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
r1_mean_readlength_clean Float Mean read length of clean forward reads TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
r1_mean_readlength_raw Float Mean read length of raw forward reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
r2_mean_q_clean Float Mean quality score of clean reverse reads TheiaProk_Illumina_PE
r2_mean_q_raw Float Mean quality score of raw reverse reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
r2_mean_readlength_clean Float Mean read length of clean reverse reads TheiaProk_Illumina_PE
r2_mean_readlength_raw Float Mean read length of raw reverse reads TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
racon_version String Version of Racon used TheiaEuk_ONT, TheiaProk_ONT
rasusa_read1_subsampled File Subsampled read file from Rasusa TheiaViral_ONT
rasusa_read2_subsampled File Subsampled read file from Rasusa (paired file) TheiaViral_ONT
rasusa_version String Version of RASUSA used for the analysis RASUSA, TheiaEuk_Illumina_PE, TheiaProk_ONT, TheiaViral_ONT
rasusa_wf_analysis_date String Date of analysis RASUSA
rasusa_wf_version String Version of PHB used for the analysis RASUSA
raven_denovo_docker String Docker image used for Raven TheiaViral_ONT
raven_denovo_status String Status of Raven assembly TheiaViral_ONT
raven_denovo_version String Version of Raven used TheiaViral_ONT
read1 File File containing the forward reads BaseSpace_Fetch, SRA_Fetch
read1_aligned String Forward read file of only aligned reads TheiaCoV_Illumina_PE, TheiaCoV_ONT
read1_aligned File Forward read file of only aligned reads TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE
read1_clean File Forward read file after quality trimming and adapter removal Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Panel
read1_concatenated File Concatenated forward reads Concatenate_Illumina_Lanes, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
read1_dehosted File The dehosted forward reads file; suggested read file for SRA submission Freyja_FASTQ, NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_ONT, TheiaMeta_Illumina_PE
read1_mapped File The mapped forward reads to the assembly TheiaMeta_Illumina_PE
read1_renamed File New read1 FASTQ file renamed to desired filename Rename_FASTQ
read1_subsampled File Read1 FASTQ files downsampled to desired coverage RASUSA, TheiaEuk_Illumina_PE
read1_trimmed File Forward read file after quality trimming and adapter removal TheiaCoV_ONT
read1_unaligned File Forward read file of unaligned reads TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
read1_unmapped File The unmapped forwards reads to the assembly TheiaMeta_Illumina_PE
read2 File File containing the reverse reads (not available for single-end or ONT data) BaseSpace_Fetch, SRA_Fetch
read2_aligned String Reverse read file of only aligned reads TheiaCoV_Illumina_PE
read2_clean File Reverse read file after quality trimming and adapter removal Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaViral_Panel
read2_concatenated File Concatenated reverse reads Concatenate_Illumina_Lanes, TheiaProk_Illumina_PE
read2_dehosted File The dehosted reverse reads file; suggested read file for SRA submission Freyja_FASTQ, NCBI_Scrub_PE, TheiaCoV_Illumina_PE, TheiaMeta_Illumina_PE
read2_mapped File The mapped reverse reads to the assembly TheiaMeta_Illumina_PE
read2_renamed File New read2 FASTQ file renamed to desired filename Rename_FASTQ
read2_subsampled File Read2 FASTQ files downsampled to desired coverage RASUSA, TheiaEuk_Illumina_PE
read2_unaligned File Reverse read file of unaligned reads TheiaCoV_Illumina_PE
read2_unmapped File The unmapped reverse reads to the assembly TheiaMeta_Illumina_PE
read_mapping_cov_hist File Coverage histogram from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_cov_stats File Coverage statistics from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_coverage Float Average coverage from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_date String Date of read mapping analysis TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_depth Float Average depth from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_flagstat File Flagstat file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_meanbaseq Float Mean base quality from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_meanmapq Float Mean mapping quality from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_percentage_mapped_reads Float Percentage of clean reads that mapped to the reference genome TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_report File Report file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_samtools_version String Version of samtools used in read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_statistics File Statistics file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_screen_clean String PASS or FAIL result from clean read screening; FAIL accompanied by the reason(s) for failure 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
read_screen_clean_tsv File Clean read screening report TSV depicting read counts, total read base pairs, and estimated genome length 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
read_screen_raw String PASS or FAIL result from raw read screening; FAIL accompanied by the reason(s) for failure TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
read_screen_raw_tsv File Raw read screening report TSV depicting read counts, total read base pairs, and estimated genome length TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
rename_fastq_files_analysis_date String Date of analysis Rename_FASTQ
rename_fastq_files_version String Version of PHB used for the analysis Rename_FASTQ
resfinder_db_version String Version of ResFinder database TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_docker String ResFinder docker image used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_pheno_table File Table containing al AMR phenotypes TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_pheno_table_species File Table with species-specific AMR phenotypes TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_pointfinder_pheno_table File TSV showing presence(1)/absence(0) of predicted resistance against an antibiotic class TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_pointfinder_results File Predicted point mutations, grouped by the gene they occur in TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_pheno_resistance String Semicolon delimited list of antimicrobial drugs and associated genes and/or point mutations. `<drug1>: <gene1>, <gene1>, <point_mutation1>; <drug2>: <gene3>, <gene4>;` TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Amp String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Ampicillin based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Axo String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Ceftriaxone based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Azm String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Azithromycin based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Cip String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Ciprofloxacin based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_quinolone String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to quinolone-class drugs based on ResFinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_quinolone_mechanisms Int The number of unique resistance mechanisms identified that confer resistance to quinolone-class drugs TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Smx String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Sulfamethoxazole based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_resistance_Tmp String States either "Resistance" followed by a semicolon delimited list of drugs and associated genes and/or point mutations or "No resistance predicted" to Trimothoprim based on Resfinder and/or PointFinder phenotypic predictions TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_predicted_xdr_shigella String Final prediction of XDR Shigella status based on CDC definition. Explanation can be found in the description above this table. TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_results File Predicted resistance genes grouped by antibiotic class TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_seqs File FASTA of resistance gene sequences from user’s input sequence TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
resfinder_version String The version of ResFinder used TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
samtools_docker String The Docker image of samtools TheiaMeta_Illumina_PE
samtools_version String The version of SAMtools used to sort and index the alignment file Clair3_Variants_ONT, Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaMeta_Illumina_PE
samtools_version_consensus String The version of SAMtools used to create the pileup before running iVar consensus TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
samtools_version_primtrim String The version of SAMtools used to create the pileup before running iVar trim Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
samtools_version_stats String The version of SAMtools used to assess the quality of read mapping TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE
sc2_s_gene_mean_coverage Float Mean read depth for the S gene in SARS-CoV-2 Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
sc2_s_gene_percent_coverage Float Percent coverage of the S gene in SARS-CoV-2 Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
semibin_bins Array[File] An array of binned metagenomic assembled genome files TheiaMeta_Illumina_PE