Question: JGI databases vs GenBank
0
gravatar for mschmid
19 months ago by
mschmid150
Switzerland
mschmid150 wrote:

I am really confused about this

Do the JGI databases contain genome assemblies which are NOT deposited on NCBI GenBank?

If yes, how can I retrieve them? Both systems seem really redundant to me doing their own thing for the same purpose.

So basically I want to fetch all bacterial genome assemblies which are ONLY available via JGI / IGM. The rest I get from GenBank which is fairly easy.

img jgi ncbi • 565 views
ADD COMMENTlink modified 19 months ago by Juke344.8k • written 19 months ago by mschmid150
2
gravatar for Juke34
19 months ago by
Juke344.8k
Sweden
Juke344.8k wrote:

Do the JGI databases contain genome assemblies which are NOT deposited on NCBI GenBank?

Yes. JGI is not part of the INSDC so it is not sync with NCBI.

If yes, how can I retrieve them? Both systems seem really redundant to me doing their own thing for the same purpose.

They don't do the same thing. NCBI is part of INSDC so data deposited there are checked and have to follow specific rules and must contain specific metadata to be sync properly with EBI and DDBJ. To my mind JGI is a bit more like "dropbox" you deposit your data in a folder and describe it. There is no sanity check about what is really in your file. I recently discussed with people from JGI, they plan to transfer data they have to INSDC when is possible. And try to minimise redundancy to not hold data that are already in INSDC.

So basically I want to fetch all bacterial genome assemblies which are ONLY available via JGI / IGM.

Sorry I don't know how to do that. You should probably create a new post for this specific question.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Juke344.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1702 users visited in the last hour