Hi, I have a list of NCBI GCA/GCF identifiers for many (hundreds of) vertebrate whole genomes that I would like to download. I initially tried Entrez.efetch, but have realized GCA numbers cannot be used with it, and this also may not be an efficient method for so many large genomes. I'm now looking at using ftplib or the NCBI datasets tool, but I'm new to bioinformatics and I am having trouble understanding the best approach with these. Has anyone done this, and if so, do you have example code you are willing to share? I'm hoping to do this with python/command line. Any help would be greatly appreciated, thanks!
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More information/download for datasets command line tool: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/
datasets download
Download genome, gene and virus data packages, including sequence, annotation, and metadata, as a zip file.
Refer to NCBI's [download and install](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/) documentation for information about getting started with the command-line tools.
Usage
datasets download [command]
Sample Commands
datasets download genome accession GCF_000001405.40 --chromosomes X,Y --exclude-gff3 --exclude-rna
datasets download genome taxon "bos taurus"
datasets download gene gene-id 672
datasets download gene symbol brca1 --taxon mouse
datasets download gene accession NP_000483.3
datasets download virus genome taxon sars-cov-2 --host dog
datasets download virus protein S --host dog --filename SARS2-spike-dog.zip
Available Commands
gene Download a gene data package
genome Download a genome data package
virus Download a virus data package
Flags
--filename string Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
--no-progressbar Hide progress bar
Global Flags
--api-key string Specify an NCBI API key
--debug Emit debugging info
--help Print detailed help about a datasets command
--version Print version of datasets
Use datasets download <command> --help for detailed help about a command.
try this tool： ncbi-genome-download
To the best of my knowledge it doesn't work with GCA/GCF identifiers. Deals only with taxonomic names or IDs.
Actually it's possible, see the parameter -A
usage: ncbi-genome-download [-h] [-s {refseq,genbank}] [-F FILE_FORMATS] [-l ASSEMBLY_LEVELS] [-g GENERA] [--genus GENERA] [--fuzzy-genus] [-S STRAINS] [-T SPECIES_TAXIDS] [-t TAXIDS] [-A ASSEMBLY_ACCESSIONS]
[-R REFSEQ_CATEGORIES] [--refseq-category REFSEQ_CATEGORIES] [-o OUTPUT] [--flat-output] [-H] [-P] [-u URI] [-p N] [-r N] [-m METADATA_TABLE] [-n] [-N] [-v] [-d] [-V]
[-M TYPE_MATERIALS]
groups
eg： ncbi-genome-download --formats "fasta,gff" -A GCF.txt --parallel 6 plant
Thanks, always something new to learn.
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There are
how toguides available about how to use NCBIdatasetscommand line tool: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/ with one specifically for large genomes : https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/