genome

Print coronavirus genome metadata by accession or taxon

Name

datasets summary virus genome - Print coronavirus genome metadata by accession or taxon

Description

Print coronavirus genome metadata (data report) by nucleotide accession or taxon. The data report is returned in JSON Lines format.

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

Examples

  datasets summary virus genome accession NC_045512.2
  datasets summary virus genome taxon SARS-COV-2 --host dog

Options

  -a, --annotated               Only include viral genomes with annotation
      --api-key string          NCBI Datasets API Key
      --as-json-lines           Stream results as newline delimited JSON-Lines
      --complete-only           only include complete coronavirus data reports
      --geo-location string     limit to coronavirus genomes isolated from a specified geographic location (continent, country or U.S. state)
  -h, --help                    help for genome
      --host string             limit to coronavirus genomes isolated from a specified host (NCBI Taxonomy ID, scientific or common name at any taxonomic rank)
      --limit string            limit the number of genome summaries returned
                                	* "all": returns all matching virus data reports
                                	* "none": returns only the number of matching virus data reports
                                	* a number: returns the specified number of matching data reports
                                	 (default "all")
      --lineage string          limit to SARS-CoV-2 genomes classified as the specified lineage (variant) by pangolin using the pangoLEARN algorithm
      --no-progressbar          hide progress bar
      --refseq                  limit to RefSeq coronavirus genomes
      --released-since string   limit to coronavirus genomes released after a specified date (MM/DD/YYYY)

Fields

MnemonicName
annotinfo-busco-completeAnnotation Info BUSCO Complete
annotinfo-busco-duplicatedAnnotation Info BUSCO Duplicated
annotinfo-busco-fragmentedAnnotation Info BUSCO Fragmented
annotinfo-busco-lineageAnnotation Info BUSCO Lineage
annotinfo-busco-missingAnnotation Info BUSCO Missing
annotinfo-busco-singlecopyAnnotation Info BUSCO Single Copy
annotinfo-busco-totalcountAnnotation Info BUSCO Total Count
annotinfo-busco-verAnnotation Info BUSCO Version
annotinfo-featcount-gene-non-codingAnnotation Info Count Gene Non-coding
annotinfo-featcount-gene-otherAnnotation Info Count Gene Other
annotinfo-featcount-gene-protein-codingAnnotation Info Count Gene Protein-coding
annotinfo-featcount-gene-pseudogeneAnnotation Info Count Gene Pseudogene
annotinfo-featcount-gene-totalAnnotation Info Count Gene Total
annotinfo-nameAnnotation Info Name
annotinfo-release-dateAnnotation Info Release Date
annotinfo-report-urlAnnotation Info Report URL
annotinfo-sourceAnnotation Info Source
assminfo-accessionAssembly Accession
assminfo-atypicalis-atypicalAssembly Atypical Is Atypical
assminfo-atypicalwarningsAssembly Atypical Warnings
assminfo-bioproject-lineage-accessionAssembly BioProject Lineage Accession
assminfo-bioproject-lineage-parent-accessionsAssembly BioProject Lineage Parent Accessions
assminfo-bioproject-lineage-titleAssembly BioProject Lineage Title
assminfo-biosample-accessionAssembly BioSample Accession
assminfo-biosample-attribute-nameAssembly BioSample Attribute Name
assminfo-biosample-attribute-valueAssembly BioSample Attribute Value
assminfo-biosample-bioproject-accessionAssembly BioSample BioProject Accession
assminfo-biosample-bioproject-parent-accessionsAssembly BioSample BioProject Parent Accessions
assminfo-biosample-bioproject-titleAssembly BioSample BioProject Title
assminfo-biosample-description-commentAssembly BioSample Description Comment
assminfo-biosample-description-organism-common-nameAssembly BioSample Description Organism Common Name
assminfo-biosample-description-organism-organism-nameAssembly BioSample Description Organism Organism Name
assminfo-biosample-description-organism-pangolinAssembly BioSample Description Organism Pangolin Classification
assminfo-biosample-description-organism-strainAssembly BioSample Description Organism Strain
assminfo-biosample-description-organism-tax-idAssembly BioSample Description Organism Taxonomic ID
assminfo-biosample-description-titleAssembly BioSample Description Title
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-last-updatedAssembly BioSample Last updated
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-publication-dateAssembly BioSample Publication date
assminfo-biosample-status-statusAssembly BioSample Status Status
assminfo-biosample-status-whenAssembly BioSample Status When
assminfo-biosample-submission-dateAssembly BioSample Submission date
assminfo-blast-urlAssembly Blast URL
assminfo-current-accessionAssembly Current Accession
assminfo-descriptionAssembly Description
assminfo-genbank-assm-accessionAssembly GenBank Accession
assminfo-levelAssembly Level
assminfo-linked-assmaccessionAssembly Linked Assembly Accession
assminfo-linked-assmtypeAssembly Linked Assembly Type
assminfo-nameAssembly Name
assminfo-paired-assmaccessionAssembly Paired Assembly Accession
assminfo-paired-assmnameAssembly Paired Assembly Name
assminfo-paired-assmstatusAssembly Paired Assembly Status
assminfo-paired_accessionAssembly Paired Accession
assminfo-refseq-assm-accessionAssembly RefSeq Accession
assminfo-refseq-categoryAssembly Refseq Category
assminfo-sequencing-techAssembly Sequencing Tech
assminfo-statusAssembly Status
assminfo-submission-dateAssembly Submission Date
assminfo-submitterAssembly Submitter
assminfo-typeAssembly Type
assminfo-ucsc-assm-nameAssembly UCSC Assembly Name
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-number-of-component-sequencesAssembly Stats Number of Component Sequences
assmstats-number-of-contigsAssembly Stats Number of Contigs
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
breedBreed
common-nameCommon name
cultivarCultivar
ecotypeEcotype
isolateIsolate
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-nameOrganism name
sexSex
strainStrain
tax-idTaxonomic ID
wgs-contigs-urlWGS contigs URL
wgs-project-accessionWGS project accession
wgs-urlWGS URL

Commands


taxon

Print coronavirus genome metadata by accession

accession

Print coronavirus genome metadata by accession

Generated June 24, 2022