How to download all the bacteria genomes from NCBI?

Question

[anran04100]

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt

I download the assembly_summary.txt

awk -F '\t' '{if($12=="Complete Genome") print $20}' assembly_summary_path.txt > assembly_summary_complete_genomes_path.txt

select Complete Genome to a new file which save the path of bacteria

but it turns out that the path file includes 21272 rows I wonder if there should be 3000+ rows since there are 3000+ bacteria in NCBI What's wrong with it? How can I download all the bacteria genomes from NCBI?

Thanks!

[shenwei356]

http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/

Answer 1

[GenoMax]

Use ncbi-genome-download tool from Kai Blin. You probably should look at the assembly levels (complete) and perhaps RefSeq category to download only complete, high-quality genomes. There is a lot of redundancy within species because of strains etc.

[shenwei356]

Right, the tool is great!