getGenome | R Documentation |
Main genome retrieval function for an organism of interest.
By specifying the scientific name of an organism of interest the
corresponding fasta-file storing the genome of the organism of interest
can be downloaded and stored locally. Genome files can be retrieved from
several databases. In addition, the genome summary statistics for the
retrieved species is stored locally to provide users with
insights regarding the genome assembly quality (see summary_genome
for details).
This is useful when comparing genomes with large difference in genome assembly qualities.
getGenome(
db = "refseq",
organism,
reference = FALSE,
skip_bacteria = TRUE,
release = NULL,
gunzip = FALSE,
path = file.path("_ncbi_downloads", "genomes"),
assembly_type = "toplevel",
mute_citation = FALSE,
analyse_genome = FALSE
)
db |
a character string specifying the database from which the genome shall be retrieved:
|
organism |
Organism selector id, there are three options to characterize an organism:
|
reference |
a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome. |
skip_bacteria |
Due to its enormous dataset size (> 700MB as of July 2023),
the bacterial summary file will not be loaded by default anymore. If users
wish to gain insights for the bacterial kingdom they needs to actively specify |
release |
a numeric, the database release version of ENSEMBL ( |
gunzip |
a logical, indicating whether or not files should be unzipped. |
path |
character, default location is paste0("set_", toupper(type)) |
assembly_type |
character, default c("primary_assembly", "toplevel"). Used for ensembl only, specifies the genome assembly type. Searches for both primary and toplevel, and if both are found, uses the first by order (so primary is prioritized by default). The Primary assembly should usually be used if it exists. The "primary assembly" contains all the top-level sequence regions, excluding alternative haplotypes and patches. If the primary assembly file is not present for a species (only defined for standard model organisms), that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: ensembl tutorial |
mute_citation |
logical, default FALSE, indicating whether citation message should be muted. |
analyse_genome |
logical, default FALSE. If TRUE, get general genome statistics like gc content etc. For more details, see ?summary_genome |
Internally this function loads the the overview.txt file from NCBI:
refseq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/
genbank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/
and creates a directory relative to file type, if you get fasta genomes it will be _ncbi_downloads/genomes'. In case the corresponding fasta file already exists within the '_ncbi_downloads/genomes' folder and is accessible within the workspace, no download process will be performed. For other file types the same rule applies.
File path to downloaded genome.
Hajk-Georg Drost
Other getBio:
getBio()
,
getCDS()
,
getCollection()
,
getGFF()
,
getProteome()
,
getRNA()
Other genome:
getGenomeSet()
,
read_genome()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.