Home > Bioinformatics, BLAST > Downloading complete genomes from ncbi ftp (from terminal)

Downloading complete genomes from ncbi ftp (from terminal)

First,

Open Terminal

Second,

Connect to NCBI genome FTP

$ftp ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

Third,

Check out the list of genomes

ftp>ls

Fourth,

cd into the directory of your organism

ftp>cd <favorite_microbe>
 Fifth,
download the file you desire using mget
ftp>mget *.gbk
which will result in
mget *.gbk [anpqy?]?

type y and enter and the file will be downloaded in your computer (at the same directory from where you connected to ftp)

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Categories: Bioinformatics, BLAST
  1. October 29, 2012 at 3:24 am

    Hi, thanks for the helpful tip. What if I need to download a bunch of sequences? Will I be able to do that using the terminal too?

  2. October 29, 2012 at 11:58 am

    Are you looking for sequence hits? That might not be possible, but if you are looking for a dataset thats available, it could be. Can you be little more specific on what type of sequence are you talking about?

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