How can I quickly download all available sequence data for a long list of organisms?

Question

[chiasmata]

I have a list of ~200 bacterial species names and I would like to download all of the available sequences for each species in FASTA format.

Is there a way of automating this process?

Answer 1

[bio_boris]

These may help

• http://nsaunders.wordpress.com/2013/05/28/how-to-bulk-retrieval-of-archaeal-genome-sequences-from-the-ncbi-ftp-site/
• Download All The Bacterial Genomes From Ncbi

Answer 2

[5heikki]

wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.*

Although maybe you just want the fna or faa file. Check the summary file too..