Rahul Nayak
A Bioinformatician
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Download genomes in batch from NCBI
By Rahul Nayak 2495 days ago
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file
