Download from NCBI RefSeq

download_refseq.sh

#!/bin/bash

set -e

rsync \
	-a \
	-m \
	--copy-links \
	--recursive \
	--times \
	--verbose \
	--exclude "all_assembly_versions/" \
	--exclude "representative/" \
	--exclude "*_cds_from_genomic.fna.gz" \
	--exclude "*_rna_from_genomic.fna.gz" \
	--include="*/" \
	--include='*genomic.fna.gz' \
	--exclude='*' \
	rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/ ncbi_refseq_bacteria/