Download genome complete referenc with Taxid or Name with comand line

Question

[Joey]

Hi,

How could I download by command line, a reference genomes with name or taxid, as *.fna file from https://www.ncbi.nlm.nih.gov/datasets/genomes/ assembly level complete or chromosome?

I want to build a kraken2 db automatically.

Thanks

Answer 1

[GenoMax]

Use genome_updater: https://github.com/pirovc/genome_updater.

NCBI datasets should also work: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/