Get summary statistics for genomes on NCBI using the NCBI Datasets API

Usage

get_genome_stats(taxon = NULL, filters = NULL)

Arguments

taxon: Taxon for which summary statistics will be retrieved, either as a character scalar (e.g., "brassicaceae") or as a numeric scalar representing NCBI Taxonomy ID (e.g., 3700).
filters: (optional) A list of filters to use when querying the API in the form of key-value pairs, with keys in list names and values in list elements (e.g., list(filters.reference_only = "true"), see examples for details).

Value

A data frame with the following variables:

accession: character, accession number.
source: character, data source.
species_taxid: numeric, NCBI Taxonomy ID.
species_name: character, species' scientific name.
species_common_name: character, species' common name.
species_ecotype: character, species' ecotype.
species_strain: character, species' strain.
species_isolate: character, species' isolate.
species_cultivar: character, species' cultivar.
assembly_level: factor, assembly level ("Complete", "Chromosome", "Scaffold", or "Contig").
assembly_status: character, assembly status.
assembly_name: character, assembly name.
assembly_type: character, assembly type.
submission_date: character, submission date (YYYY-MM-DD).
submitter: character, submitter name.
sequencing_technology: character, sequencing technology.
atypical: logical, indicator of wheter the genome is atypical.
refseq_category: character, RefSeq category.
chromosome_count: numeric, number of chromosomes.
sequence_length: numeric, total sequence length.
ungapped_length: numeric, ungapped sequence length.
contig_count: numeric, number of contigs.
contig_N50: numeric, contig N50.
contig_L50: numeric, contig L50.
scaffold_N50: numeric, contig N50.
scaffold_L50: numeric, contig L50.
GC_percent: numeric, GC percentage (0-100).
annotation_provider: character, name of annotation provider.
annotation_release_date: character, annotation release date (YYYY-MM-DD).
gene_count_total: numeric, total number of genes.
gene_count_coding: numeric, number of protein-coding genes.
gene_count_noncoding: numeric, number of non-coding genes.
gene_count_pseudogene: numeric, number of pseudogenes.
gene_count_other: numeric, number of other genes.
CC_ratio: numeric, ratio of the number of contigs to the number of chromosomes.

Details

Possible filters for the filters parameter can be accessed at https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/genome/taxon/-taxons-/dataset_report.

Examples

# Example 1: Search for A. thaliana genomes by tax ID
ex1 <- get_genome_stats(taxon = 3702)

# Example 2: Search for A. thaliana genomes by name
ex2 <- get_genome_stats(taxon = "Arabidopsis thaliana")

# Example 3: Search for chromosome-level Brassicaeae genomes
ex3 <- get_genome_stats(
    taxon = "brassicaceae",
    filters = list(filters.assembly_level = "chromosome")
)