I am trying to extract information about SNP data from the FTP server of NCBI. Could someone please explain to me how the directory is organised? There are many many files and folders and I can't figure which contains what. Is there one file which explains the organisation of the ftp site properly? The NCBI help manual did not give much help beyond helping me find species of interest.

  • $\begingroup$ Is this the help that your talking about? It is perfectly clear. What can you not figure out? $\endgroup$
    Jun 7, 2014 at 4:11
  • $\begingroup$ just a thought - its better to use biopython or some other script library to get what you want, especially if you are trying to get more than one item. $\endgroup$
    – shigeta
    Aug 2, 2014 at 15:12

1 Answer 1


Getting SNP data from FTP Site of NCBI SNP:

It's actually simple to download the data from the NCBI, if you follow the method given by FAQ( as given by @WYSIWYG).

Step 1:

Goto organism FTP: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/

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Step 2

Open your required organism folder:

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From here you can download any file you wanted. If you trying to study the whole organism please download any one of the whole folders(ASN.1, rs_fasta, XML(recommended)).


It's not about the downloading it's about understanding the files which are provided.

files types:

All of them contents almost the same data, just in different format. It's up to you how your script(preferably Python or Perl) works to get out the import information.

Other way of Download from NCBI FTP:

You can always use filezilla:

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