Understanding the refseq ftp file

0

Entering edit mode

9.7 years ago

jeremy.cox.2 ▴ 130

I set out to download and compile the complete refseq bacteria database.

I download from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria/

*.genomic.fna.gz files

After decompresion, the files total ~100 GB. Whereas my nt bacterial database is only 12 GB. And I expect refseq to be smaller than nt. So I think I have misunderstood what I want to download.

Can you help me figure out what files or how to know what files I actually want? I am doing the same for viruses and fungi.

refseq ncbi • 3.6k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by jeremy.cox.2 ▴ 130

0

Entering edit mode

This seems strange. Are you sure the bacterial nt database was downloaded accurately?

ADD REPLY • link 9.7 years ago by Ram 44k

1

Entering edit mode

nt is non-redundant, refseq genomic is not. Just check how huge the refseq_genomic blast db is in comparison to nt (26 tar.gz vs 152 tar.gz files)..

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by 5heikki 11k

0

Entering edit mode

Yes, I downloaded the NT database correctly. I downloaded a single "nt.fa" file, compressed.

It would seem that the total size of the refseq_genomic blast db ~26 GB, so clearly I have downloaded the WRONG FILES.

This question is how do I know which files are the correct files?

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by jeremy.cox.2 ▴ 130

0

Entering edit mode

Are you sure it's just 26 GB? In the ftp, there are 152 ~0.9GB refseq_genomic tar.gz files. Surely uncompromising them makes it even bigger, i.e. over ~136 GB.

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by 5heikki 11k

Login before adding your answer.