genome

Convert Genome Assembly Data Report into TSV format

genome

Convert Genome Assembly Data Report into TSV format

Name

dataformat tsv genome - Convert Genome Assembly Data Report into TSV format

Synopsis

dataformat tsv genome [flags]

Description

Convert Genome Assembly Data Report into TSV format.

Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.

Examples

  dataformat tsv genome --inputfile human/ncbi_dataset/data/assembly_data_report.jsonl
  dataformat tsv genome --package human.zip

Options

      --elide-header       Do not output header
      --fields strings     Comma-separated list of fields
      --force              Force dataformat to run without type check prompt
  -h, --help               help for genome
      --inputfile string   Input file (default "/dev/stdin")
      --package string     Data package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
accessionAssembly Accession
ani-best-ani-match-aniANI Best ANI match ANI
ani-best-ani-match-assemblyANI Best ANI match Assembly
ani-best-ani-match-assembly_coverageANI Best ANI match Assembly Coverage
ani-best-ani-match-categoryANI Best ANI match Type Category
ani-best-ani-match-organismANI Best ANI match Organism
ani-best-ani-match-type_assembly_coverageANI Best ANI match Type Assembly Coverage
ani-best-match-statusANI Best match status
ani-categoryANI Category
ani-check-statusANI Check status
ani-commentANI Comment
ani-submitted-ani-match-aniANI Declared ANI match ANI
ani-submitted-ani-match-assemblyANI Declared ANI match Assembly
ani-submitted-ani-match-assembly_coverageANI Declared ANI match Assembly Coverage
ani-submitted-ani-match-categoryANI Declared ANI match Type Category
ani-submitted-ani-match-organismANI Declared ANI match Organism
ani-submitted-ani-match-type_assembly_coverageANI Declared ANI match Type Assembly Coverage
ani-submitted-organismANI Submitted organism
ani-submitted-speciesANI Submitted species
annotinfo-busco-completeAnnotation BUSCO Complete
annotinfo-busco-duplicatedAnnotation BUSCO Duplicated
annotinfo-busco-fragmentedAnnotation BUSCO Fragmented
annotinfo-busco-lineageAnnotation BUSCO Lineage
annotinfo-busco-missingAnnotation BUSCO Missing
annotinfo-busco-singlecopyAnnotation BUSCO Single Copy
annotinfo-busco-totalcountAnnotation BUSCO Total Count
annotinfo-busco-verAnnotation BUSCO Version
annotinfo-featcount-gene-non-codingAnnotation Count Gene Non-coding
annotinfo-featcount-gene-otherAnnotation Count Gene Other
annotinfo-featcount-gene-protein-codingAnnotation Count Gene Protein-coding
annotinfo-featcount-gene-pseudogeneAnnotation Count Gene Pseudogene
annotinfo-featcount-gene-totalAnnotation Count Gene Total
annotinfo-methodAnnotation Method
annotinfo-nameAnnotation Name
annotinfo-pipelineAnnotation Pipeline
annotinfo-providerAnnotation Provider
annotinfo-release-dateAnnotation Release Date
annotinfo-report-urlAnnotation Report URL
annotinfo-software-versionAnnotation Software Version
annotinfo-statusAnnotation Status
assminfo-assembly-methodAssembly Assembly Method
assminfo-atypicalis-atypicalAssembly Atypical Is Atypical
assminfo-atypicalwarningsAssembly Atypical Warnings
assminfo-bioprojectAssembly BioProject Accession
assminfo-bioproject-lineage-accessionAssembly BioProject Lineage Accession
assminfo-bioproject-lineage-parent-accessionAssembly BioProject Lineage Parent Accession
assminfo-bioproject-lineage-parent-accessionsAssembly BioProject Lineage Parent Accessions
assminfo-bioproject-lineage-titleAssembly BioProject Lineage Title
assminfo-biosample-accessionAssembly BioSample Accession
assminfo-biosample-ageAssembly BioSample Age
assminfo-biosample-attribute-nameAssembly BioSample Attribute Name
assminfo-biosample-attribute-valueAssembly BioSample Attribute Value
assminfo-biosample-biomaterial-provider-Assembly BioSample Biomaterial provider
assminfo-biosample-bioproject-accessionAssembly BioSample BioProject Accession
assminfo-biosample-bioproject-parent-accessionAssembly BioSample BioProject Parent Accession
assminfo-biosample-bioproject-parent-accessionsAssembly BioSample BioProject Parent Accessions
assminfo-biosample-bioproject-titleAssembly BioSample BioProject Title
assminfo-biosample-breedAssembly BioSample Breed
assminfo-biosample-collected-byAssembly BioSample Collected by
assminfo-biosample-collection-dateAssembly BioSample Collection date
assminfo-biosample-cultivarAssembly BioSample Cultivar
assminfo-biosample-description-commentAssembly BioSample Description Comment
assminfo-biosample-description-organism-common-nameAssembly BioSample Description Organism Common Name
assminfo-biosample-description-organism-infraspecific-breedAssembly BioSample Description Organism Infraspecific Names Breed
assminfo-biosample-description-organism-infraspecific-cultivarAssembly BioSample Description Organism Infraspecific Names Cultivar
assminfo-biosample-description-organism-infraspecific-ecotypeAssembly BioSample Description Organism Infraspecific Names Ecotype
assminfo-biosample-description-organism-infraspecific-isolateAssembly BioSample Description Organism Infraspecific Names Isolate
assminfo-biosample-description-organism-infraspecific-sexAssembly BioSample Description Organism Infraspecific Names Sex
assminfo-biosample-description-organism-infraspecific-strainAssembly BioSample Description Organism Infraspecific Names Strain
assminfo-biosample-description-organism-nameAssembly BioSample Description Organism Name
assminfo-biosample-description-organism-pangolinAssembly BioSample Description Organism Pangolin Classification
assminfo-biosample-description-organism-tax-idAssembly BioSample Description Organism Taxonomic ID
assminfo-biosample-description-titleAssembly BioSample Description Title
assminfo-biosample-development-stageAssembly BioSample Development stage
assminfo-biosample-ecotypeAssembly BioSample Ecotype
assminfo-biosample-geo-loc-nameAssembly BioSample Geographic location
assminfo-biosample-hostAssembly BioSample Host
assminfo-biosample-host-diseaseAssembly BioSample Host disease
assminfo-biosample-identified-byAssembly BioSample Identified by
assminfo-biosample-ids-dbAssembly BioSample Sample Identifiers Database
assminfo-biosample-ids-labelAssembly BioSample Sample Identifiers Label
assminfo-biosample-ids-valueAssembly BioSample Sample Identifiers Value
assminfo-biosample-ifsac-categoryAssembly BioSample IFSAC category
assminfo-biosample-isolateAssembly BioSample Isolate
assminfo-biosample-isolate-name-aliasAssembly BioSample Isolate name alias
assminfo-biosample-isolation-sourceAssembly BioSample Isolation source
assminfo-biosample-last-updatedAssembly BioSample Last updated
assminfo-biosample-lat-lonAssembly BioSample Latitude / Longitude
assminfo-biosample-modelsAssembly BioSample Models
assminfo-biosample-owner-contact-labAssembly BioSample Owner Contact Lab
assminfo-biosample-owner-nameAssembly BioSample Owner Name
assminfo-biosample-packageAssembly BioSample Package
assminfo-biosample-project-nameAssembly BioSample Project name
assminfo-biosample-publication-dateAssembly BioSample Publication date
assminfo-biosample-sample-nameAssembly BioSample Sample name
assminfo-biosample-serotypeAssembly BioSample Serotype
assminfo-biosample-serovarAssembly BioSample Serovar
assminfo-biosample-sexAssembly BioSample Sex
assminfo-biosample-source-typeAssembly BioSample Source type
assminfo-biosample-status-statusAssembly BioSample Status Status
assminfo-biosample-status-whenAssembly BioSample Status When
assminfo-biosample-strainAssembly BioSample Strain
assminfo-biosample-sub-speciesAssembly BioSample Sub-species
assminfo-biosample-submission-dateAssembly BioSample Submission date
assminfo-biosample-tissueAssembly BioSample Tissue
assminfo-blast-urlAssembly Blast URL
assminfo-descriptionAssembly Description
assminfo-grouping-methodAssembly Grouping Method
assminfo-levelAssembly Level
assminfo-linked-assm-accessionAssembly Linked Assembly Accession
assminfo-linked-assm-typeAssembly Linked Assembly Type
assminfo-long-nameAssembly LongName
assminfo-nameAssembly Name
assminfo-notesAssembly Notes
assminfo-paired-assm-accessionAssembly Paired Assembly Accession
assminfo-paired-assm-changedAssembly Paired Assembly Changed
assminfo-paired-assm-manual-diffAssembly Paired Assembly Manual Diff
assminfo-paired-assm-nameAssembly Paired Assembly Name
assminfo-paired-assm-only-genbankAssembly Paired Assembly Only Genbank
assminfo-paired-assm-only-refseqAssembly Paired Assembly Only RefSeq
assminfo-paired-assm-statusAssembly Paired Assembly Status
assminfo-refseq-categoryAssembly Refseq Category
assminfo-release-dateAssembly Release Date
assminfo-sequencing-techAssembly Sequencing Tech
assminfo-statusAssembly Status
assminfo-submitterAssembly Submitter
assminfo-suppression-reasonAssembly Suppression Reason
assminfo-synonymAssembly Synonym
assminfo-typeAssembly Type
assmstats-contig-l50Assembly Stats Contig L50
assmstats-contig-n50Assembly Stats Contig N50
assmstats-gaps-between-scaffolds-countAssembly Stats Gaps Between Scaffolds Count
assmstats-gc-countAssembly Stats GC Count
assmstats-gc-percentAssembly Stats GC Percent
assmstats-genome-coverageAssembly Stats Genome Coverage
assmstats-number-of-component-sequencesAssembly Stats Number of Component Sequences
assmstats-number-of-contigsAssembly Stats Number of Contigs
assmstats-number-of-organellesAssembly Stats Number of Organelles
assmstats-number-of-scaffoldsAssembly Stats Number of Scaffolds
assmstats-scaffold-l50Assembly Stats Scaffold L50
assmstats-scaffold-n50Assembly Stats Scaffold N50
assmstats-total-number-of-chromosomesAssembly Stats Total Number of Chromosomes
assmstats-total-sequence-lenAssembly Stats Total Sequence Length
assmstats-total-ungapped-lenAssembly Stats Total Ungapped Length
checkm-completenessCheckM completeness
checkm-completeness-percentileCheckM completeness percentile
checkm-contaminationCheckM contamination
checkm-marker-setCheckM marker set
checkm-marker-set-rankCheckM marker set rank
checkm-species-tax-idCheckM species tax id
checkm-versionCheckM version
current-accessionCurrent Accession
organelle-assembly-nameOrganelle Assembly Name
organelle-bioproject-accessionsOrganelle BioProject Accessions
organelle-descriptionOrganelle Description
organelle-infraspecific-nameOrganelle Infraspecific Name
organelle-submitterOrganelle Submitter
organelle-total-seq-lengthOrganelle Total Seq Length
organism-common-nameOrganism Common Name
organism-infraspecific-breedOrganism Infraspecific Names Breed
organism-infraspecific-cultivarOrganism Infraspecific Names Cultivar
organism-infraspecific-ecotypeOrganism Infraspecific Names Ecotype
organism-infraspecific-isolateOrganism Infraspecific Names Isolate
organism-infraspecific-sexOrganism Infraspecific Names Sex
organism-infraspecific-strainOrganism Infraspecific Names Strain
organism-nameOrganism Name
organism-pangolinOrganism Pangolin Classification
organism-tax-idOrganism Taxonomic ID
source_databaseSource Database
type_material-display_textType Material Display Text
type_material-labelType Material Label
wgs-contigs-urlWGS contigs URL
wgs-project-accessionWGS project accession
wgs-urlWGS URL
Generated November 25, 2024