NCBI Datasets Virus Data Package

Sequences and metadata for a set of virus GenBank genomes or SARS-CoV-2 proteins

NCBI Datasets Virus Data Package

Sequences and metadata for a set of virus GenBank genomes or SARS-CoV-2 proteins

The NCBI Datasets Virus Data Package contains sequences and metadata for a set of requested virus GenBank genomes or SARS-CoV-2 proteins. The data package may include genome, coding sequence (CDS) and protein sequences in FASTA format, and a data report containing metadata in JSON Lines format.

Downloading the Package

You can download an NCBI Datasets Virus Data Package using the NCBI Datasets command-line tools.

Package Content

NCBI Datasets Virus Genome Data Package

datasets download virus genome taxon monkeypox --filename monkeypox.zip
unzip monkeypox.zip -d monkeypox
tree monkeypox/

monkeypox/
|-- README.md
|-- md5sum.txt
`-- ncbi_dataset
    `-- data
        |-- data_report.jsonl
        |-- dataset_catalog.json
        |-- genomic.fna
        `-- virus_dataset.md

NCBI Datasets SARS-CoV-2 Protein Data Package

(note: this package does not contain SARS-CoV-2 genome sequence)

datasets download virus protein S --filename spike-protein.zip
unzip spike-protein.zip -d spike-protein
tree spike-protein/

spike-protein/
|-- README.md
|-- md5sum.txt
`-- ncbi_dataset
    `-- data
        |-- data_report.jsonl
        |-- dataset_catalog.json
        |-- protein.faa
        `-- virus_dataset.md

Virus Data Report

The virus data report contains metadata describing the genomes and proteins in the data package. The file is in JSON Lines format, where each line is the metadata for one genome or one protein. Use the dataformat tool for easy conversion to a tabular format of selected fields.

Virus Annotation Report

The virus annotation contains metadata describing the annotated genes and proteins on the genomes in the data package. The file is in JSON Lines format, where each line is the metadata for one genome or one protein. Use the dataformat tool for easy conversion to a tabular format of selected fields.

  • Path: ncbi_dataset/data/annotation_report.jsonl
  • Schema: Virus Annotation Report (available soon)

FASTA Sequence Files

Genomic FASTA

Nucleotide sequence of the viral genome.

Example FASTA Defline:

>MW583405.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/TX-CDC-9N37-8996/2021, complete genome

CDS FASTA

Nucleotide sequence of the coding sequence of each protein and mature peptide.

Example FASTA Defline:

>NC_045512.2:21563-25384 surface glycoprotein [organism=Severe acute respiratory syndrome coronavirus 2] [isolate=Wuhan-Hu-1]

Protein FASTA

Protein sequence of each protein and mature peptide.

Example FASTA Defline:

>QMT27626.1:1-180 leader protein [polyprotein=ORF1ab polyprotein] [organism=Severe acute respiratory syndrome coronavirus 2] [isolate=SARS-CoV-2/human/USA/WA-S1488/2020]

Other files

Virus README

The virus README describes the available SARS-CoV-2 data packages, their content and options for querying.

  • Path: ncbi_dataset/data/virus_dataset.md

README.md

The README contains a general project description common to all data packages.

  • Path: README.md

Dataset catalog

The dataset catalog lists each data file contained within or referenced by this package. Each data file is associated with a content type and location.

  • Path: ncbi_dataset/dataset_catalog.json

MD5 checksum file

The MD5 checksum file contains MD5 hash values for each file contained in the data package after decompression. These hash values can be used as a checksum to verify that a file has not changed as the result of an error during download or decompression. Each line of the MD5 checksum file corresponds to a file in the package after decompression, where the first column contains the MD5 hash value and the second column contains the path to the file.

  • Path: md5sum.txt
Generated November 25, 2024