Hello Shenwiyn,

For a genome such as "nt", then you will want all of the files starting with "nt" in this directory. Use the ones ending in "md5" to double check that the download was complete for each.


If you are looking to just including the databases on the Public Main Galaxy server, there are three from this division: nt, htgs, and wgs. You can of course pick these or any others that you want for your own local.

We also include one other database, the bacteriophage *?X174*, as a sort of homage.
Read why here:
http://en.wikipedia.org/wiki/Phi_X_174
http://www.ncbi.nlm.nih.gov/pubmed/870828
You can find/download the fasta in genbank, then create the indexes with formatdb.

Hopefully this helps,

Jen
Galaxy team

On 3/5/13 5:26 PM, shenwiyn wrote:
Hi,
I have some questions about the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gz....I don't know the differents among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174.
Could anyone help me and give me some advice please? Thank you very much.
------------------------------------------------------------------------
shenwiyn


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