genome
Convert Genome Assembly Data Report into an Excel workbook
genome
Convert Genome Assembly Data Report into an Excel workbook
Name
dataformat excel genome - Convert Genome Assembly Data Report into an Excel workbook
Synopsis
dataformat excel genome [flags]
Description
Convert Genome Assembly Data Report into an Excel workbook.
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
Examples
dataformat excel genome --inputfile human/ncbi_dataset/data/assembly_data_report.jsonl --outputfile human-genomes.xlsx
dataformat excel genome --package human.zip --outputfile human-genomes.xlsx
Options
--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")
--outputfile string Excel workbook file
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| accession | Assembly Accession |
| ani-best-ani-match-ani | ANI Best ANI match ANI |
| ani-best-ani-match-assembly | ANI Best ANI match Assembly |
| ani-best-ani-match-assembly_coverage | ANI Best ANI match Assembly Coverage |
| ani-best-ani-match-category | ANI Best ANI match Type Category |
| ani-best-ani-match-organism | ANI Best ANI match Organism |
| ani-best-ani-match-type_assembly_coverage | ANI Best ANI match Type Assembly Coverage |
| ani-best-match-status | ANI Best match status |
| ani-category | ANI Category |
| ani-check-status | ANI Check status |
| ani-comment | ANI Comment |
| ani-submitted-ani-match-ani | ANI Declared ANI match ANI |
| ani-submitted-ani-match-assembly | ANI Declared ANI match Assembly |
| ani-submitted-ani-match-assembly_coverage | ANI Declared ANI match Assembly Coverage |
| ani-submitted-ani-match-category | ANI Declared ANI match Type Category |
| ani-submitted-ani-match-organism | ANI Declared ANI match Organism |
| ani-submitted-ani-match-type_assembly_coverage | ANI Declared ANI match Type Assembly Coverage |
| ani-submitted-organism | ANI Submitted organism |
| ani-submitted-species | ANI Submitted species |
| annotinfo-busco-complete | Annotation BUSCO Complete |
| annotinfo-busco-duplicated | Annotation BUSCO Duplicated |
| annotinfo-busco-fragmented | Annotation BUSCO Fragmented |
| annotinfo-busco-lineage | Annotation BUSCO Lineage |
| annotinfo-busco-missing | Annotation BUSCO Missing |
| annotinfo-busco-singlecopy | Annotation BUSCO Single Copy |
| annotinfo-busco-totalcount | Annotation BUSCO Total Count |
| annotinfo-busco-ver | Annotation BUSCO Version |
| annotinfo-featcount-gene-non-coding | Annotation Count Gene Non-coding |
| annotinfo-featcount-gene-other | Annotation Count Gene Other |
| annotinfo-featcount-gene-protein-coding | Annotation Count Gene Protein-coding |
| annotinfo-featcount-gene-pseudogene | Annotation Count Gene Pseudogene |
| annotinfo-featcount-gene-total | Annotation Count Gene Total |
| annotinfo-method | Annotation Method |
| annotinfo-name | Annotation Name |
| annotinfo-pipeline | Annotation Pipeline |
| annotinfo-provider | Annotation Provider |
| annotinfo-release-date | Annotation Release Date |
| annotinfo-report-url | Annotation Report URL |
| annotinfo-software-version | Annotation Software Version |
| annotinfo-status | Annotation Status |
| assminfo-assembly-method | Assembly Assembly Method |
| assminfo-atypicalis-atypical | Assembly Atypical Is Atypical |
| assminfo-atypicalwarnings | Assembly Atypical Warnings |
| assminfo-bioproject | Assembly BioProject Accession |
| assminfo-bioproject-lineage-accession | Assembly BioProject Lineage Accession |
| assminfo-bioproject-lineage-parent-accession | Assembly BioProject Lineage Parent Accession |
| assminfo-bioproject-lineage-parent-accessions | Assembly BioProject Lineage Parent Accessions |
| assminfo-bioproject-lineage-title | Assembly BioProject Lineage Title |
| assminfo-biosample-accession | Assembly BioSample Accession |
| assminfo-biosample-age | Assembly BioSample Age |
| assminfo-biosample-attribute-name | Assembly BioSample Attribute Name |
| assminfo-biosample-attribute-value | Assembly BioSample Attribute Value |
| assminfo-biosample-biomaterial-provider- | Assembly BioSample Biomaterial provider |
| assminfo-biosample-bioproject-accession | Assembly BioSample BioProject Accession |
| assminfo-biosample-bioproject-parent-accession | Assembly BioSample BioProject Parent Accession |
| assminfo-biosample-bioproject-parent-accessions | Assembly BioSample BioProject Parent Accessions |
| assminfo-biosample-bioproject-title | Assembly BioSample BioProject Title |
| assminfo-biosample-breed | Assembly BioSample Breed |
| assminfo-biosample-collected-by | Assembly BioSample Collected by |
| assminfo-biosample-collection-date | Assembly BioSample Collection date |
| assminfo-biosample-cultivar | Assembly BioSample Cultivar |
| assminfo-biosample-description-comment | Assembly BioSample Description Comment |
| assminfo-biosample-description-organism-common-name | Assembly BioSample Description Organism Common Name |
| assminfo-biosample-description-organism-infraspecific-breed | Assembly BioSample Description Organism Infraspecific Names Breed |
| assminfo-biosample-description-organism-infraspecific-cultivar | Assembly BioSample Description Organism Infraspecific Names Cultivar |
| assminfo-biosample-description-organism-infraspecific-ecotype | Assembly BioSample Description Organism Infraspecific Names Ecotype |
| assminfo-biosample-description-organism-infraspecific-isolate | Assembly BioSample Description Organism Infraspecific Names Isolate |
| assminfo-biosample-description-organism-infraspecific-sex | Assembly BioSample Description Organism Infraspecific Names Sex |
| assminfo-biosample-description-organism-infraspecific-strain | Assembly BioSample Description Organism Infraspecific Names Strain |
| assminfo-biosample-description-organism-name | Assembly BioSample Description Organism Name |
| assminfo-biosample-description-organism-pangolin | Assembly BioSample Description Organism Pangolin Classification |
| assminfo-biosample-description-organism-tax-id | Assembly BioSample Description Organism Taxonomic ID |
| assminfo-biosample-description-title | Assembly BioSample Description Title |
| assminfo-biosample-development-stage | Assembly BioSample Development stage |
| assminfo-biosample-ecotype | Assembly BioSample Ecotype |
| assminfo-biosample-geo-loc-name | Assembly BioSample Geographic location |
| assminfo-biosample-host | Assembly BioSample Host |
| assminfo-biosample-host-disease | Assembly BioSample Host disease |
| assminfo-biosample-identified-by | Assembly BioSample Identified by |
| assminfo-biosample-ids-db | Assembly BioSample Sample Identifiers Database |
| assminfo-biosample-ids-label | Assembly BioSample Sample Identifiers Label |
| assminfo-biosample-ids-value | Assembly BioSample Sample Identifiers Value |
| assminfo-biosample-ifsac-category | Assembly BioSample IFSAC category |
| assminfo-biosample-isolate | Assembly BioSample Isolate |
| assminfo-biosample-isolate-name-alias | Assembly BioSample Isolate name alias |
| assminfo-biosample-isolation-source | Assembly BioSample Isolation source |
| assminfo-biosample-last-updated | Assembly BioSample Last updated |
| assminfo-biosample-lat-lon | Assembly BioSample Latitude / Longitude |
| assminfo-biosample-models | Assembly BioSample Models |
| assminfo-biosample-owner-contact-lab | Assembly BioSample Owner Contact Lab |
| assminfo-biosample-owner-name | Assembly BioSample Owner Name |
| assminfo-biosample-package | Assembly BioSample Package |
| assminfo-biosample-project-name | Assembly BioSample Project name |
| assminfo-biosample-publication-date | Assembly BioSample Publication date |
| assminfo-biosample-sample-name | Assembly BioSample Sample name |
| assminfo-biosample-serotype | Assembly BioSample Serotype |
| assminfo-biosample-serovar | Assembly BioSample Serovar |
| assminfo-biosample-sex | Assembly BioSample Sex |
| assminfo-biosample-source-type | Assembly BioSample Source type |
| assminfo-biosample-status-status | Assembly BioSample Status Status |
| assminfo-biosample-status-when | Assembly BioSample Status When |
| assminfo-biosample-strain | Assembly BioSample Strain |
| assminfo-biosample-sub-species | Assembly BioSample Sub-species |
| assminfo-biosample-submission-date | Assembly BioSample Submission date |
| assminfo-biosample-tissue | Assembly BioSample Tissue |
| assminfo-blast-url | Assembly Blast URL |
| assminfo-description | Assembly Description |
| assminfo-grouping-method | Assembly Grouping Method |
| assminfo-level | Assembly Level |
| assminfo-linked-assm-accession | Assembly Linked Assembly Accession |
| assminfo-linked-assm-type | Assembly Linked Assembly Type |
| assminfo-long-name | Assembly LongName |
| assminfo-name | Assembly Name |
| assminfo-notes | Assembly Notes |
| assminfo-paired-assm-accession | Assembly Paired Assembly Accession |
| assminfo-paired-assm-changed | Assembly Paired Assembly Changed |
| assminfo-paired-assm-manual-diff | Assembly Paired Assembly Manual Diff |
| assminfo-paired-assm-name | Assembly Paired Assembly Name |
| assminfo-paired-assm-only-genbank | Assembly Paired Assembly Only Genbank |
| assminfo-paired-assm-only-refseq | Assembly Paired Assembly Only RefSeq |
| assminfo-paired-assm-status | Assembly Paired Assembly Status |
| assminfo-refseq-category | Assembly Refseq Category |
| assminfo-release-date | Assembly Release Date |
| assminfo-sequencing-tech | Assembly Sequencing Tech |
| assminfo-status | Assembly Status |
| assminfo-submitter | Assembly Submitter |
| assminfo-suppression-reason | Assembly Suppression Reason |
| assminfo-synonym | Assembly Synonym |
| assminfo-type | Assembly Type |
| assmstats-contig-l50 | Assembly Stats Contig L50 |
| assmstats-contig-n50 | Assembly Stats Contig N50 |
| assmstats-gaps-between-scaffolds-count | Assembly Stats Gaps Between Scaffolds Count |
| assmstats-gc-count | Assembly Stats GC Count |
| assmstats-gc-percent | Assembly Stats GC Percent |
| assmstats-genome-coverage | Assembly Stats Genome Coverage |
| assmstats-number-of-component-sequences | Assembly Stats Number of Component Sequences |
| assmstats-number-of-contigs | Assembly Stats Number of Contigs |
| assmstats-number-of-organelles | Assembly Stats Number of Organelles |
| assmstats-number-of-scaffolds | Assembly Stats Number of Scaffolds |
| assmstats-scaffold-l50 | Assembly Stats Scaffold L50 |
| assmstats-scaffold-n50 | Assembly Stats Scaffold N50 |
| assmstats-total-number-of-chromosomes | Assembly Stats Total Number of Chromosomes |
| assmstats-total-sequence-len | Assembly Stats Total Sequence Length |
| assmstats-total-ungapped-len | Assembly Stats Total Ungapped Length |
| checkm-completeness | CheckM completeness |
| checkm-completeness-percentile | CheckM completeness percentile |
| checkm-contamination | CheckM contamination |
| checkm-marker-set | CheckM marker set |
| checkm-marker-set-rank | CheckM marker set rank |
| checkm-species-tax-id | CheckM species tax id |
| checkm-version | CheckM version |
| current-accession | Current Accession |
| organelle-assembly-name | Organelle Assembly Name |
| organelle-bioproject-accessions | Organelle BioProject Accessions |
| organelle-description | Organelle Description |
| organelle-infraspecific-name | Organelle Infraspecific Name |
| organelle-submitter | Organelle Submitter |
| organelle-total-seq-length | Organelle Total Seq Length |
| organism-common-name | Organism Common Name |
| organism-infraspecific-breed | Organism Infraspecific Names Breed |
| organism-infraspecific-cultivar | Organism Infraspecific Names Cultivar |
| organism-infraspecific-ecotype | Organism Infraspecific Names Ecotype |
| organism-infraspecific-isolate | Organism Infraspecific Names Isolate |
| organism-infraspecific-sex | Organism Infraspecific Names Sex |
| organism-infraspecific-strain | Organism Infraspecific Names Strain |
| organism-name | Organism Name |
| organism-pangolin | Organism Pangolin Classification |
| organism-tax-id | Organism Taxonomic ID |
| source_database | Source Database |
| type_material-display_text | Type Material Display Text |
| type_material-label | Type Material Label |
| wgs-contigs-url | WGS contigs URL |
| wgs-project-accession | WGS project accession |
| wgs-url | WGS URL |