quick way to get all the fasta files for all bacterial genomes

download-genbank.sh

#!/bin/bash

set -euo pipefail

rm -rf genbank/

rsync \
        --archive \
        --progress \
        --recursive \
        --prune-empty-dirs \
        --copy-links \
        --include='*/' \
        --include='latest_assembly_versions/**annotated_assembly_genomic.fna.gz' \
        --exclude='*' \
        rsync://ftp.ncbi.nih.gov/genomes/genbank/bacteria/ \
        genbank