Is there a way to download MAG/UBA sequences from the Genbank?

[songb1230]

Dear kblin,

I like to build a database of MAG/UBA sequences reported in the papers of Parks et al 2017 (https://www.nature.com/articles/s41564-017-0012-7) and Anantharaman et al 2016 (https://www.nature.com/articles/ncomms13219). Is there a way to download the fasta and genbank files of the MAG/UBA sequences?

Thanks

BK

[kblin]

I've just looked at the Parks et al. paper, but for the UBA set there, the authors have created a BioProject at NCBI (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA348753). On that page, there's an "assembly details" table, with a download link that will give you what looks like a tab-separated format containing assembly IDs in the first column.

With a bit of scripting magic, you could turn that into an assembly ID file suitable for ncbi-genome-download. Something like this (I'm using bash, but anything that works for you is good):

# use tail to get rid of the two lines of comments on top
# then use cut to only keep the first column
tail -n +3 PRJNA348753_AssemblyDetails.txt | cut -f1 > assembly_ids.txt

Now you can use that to run ncbi-genome-download (make sure you have at least version 0.2.7 installed):

ncbi-genome-download --section genbank --assembly-accessions assembly_ids.txt bacteria,archaea

Hope this helps.

[songb1230]

Yes, it works.

Thank you

[kblin]

Let's just keep this open in case anybody else wants to do something similar.

[songb1230]

Sounds good. Thanks BK Song

…

On Jul 17, 2018, at 10:57 AM, Kai Blin ***@***.***> wrote: Let's just keep this open in case anybody else wants to do something similar. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#70 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Alyda1gVe4HvfMXLRkV5GK1CktnGebgHks5uHftGgaJpZM4VP2qS>.

[EBosi]

Hi Kai,
I read in the ncbi FAQs that the Biosample entry of MAGs should have the tag sample_type set as metagenomic assembly, is it something that can be accessed with ncbi-genome-download? If yes it would be possible to use that filter to download MAGs.

[chingciripit]

Hi Kai,

Is there a way to automate the download of PRJNA348753_AssemblyDetails.txt from the NCBI Bioproject website by using only the BioProject ID PRJNA348753 as the input?

Thanks.

Ching