diamond Feature Request: taxonomy with blast databases

Hi!

I'm just trying out the new 'blast formatted databases' feature - or, rather, I was about to try it out. However, I see that taxonomy reporting is not supported for blast databases. I'd like to request this as a feature for the future!

Thanks,

Darren

Jun 09 '21 08:06 DarrenObbard

Hi Darren, that's definitely going to happen, hopefully in the near future.

Jun 09 '21 08:06 bbuchfink

Hi Darren, that's definitely going to happen, hopefully in the near future.

Any update on this feature?

Sep 09 '22 15:09 IdoBar

It's on a long todo list, but I'll see what I can do.

Sep 11 '22 12:09 bbuchfink

Hi,

Is there any update on this, or suggestions for a workaround? I was hoping to use diamond to search a large dataset for bacteria-aligning sequences, and this is somewhat of a dead end....

Dec 13 '22 19:12 maggielawton

Is there any update on this, or suggestions for a workaround?

You can use the diamond database format which supports taxonomic information.

Dec 25 '22 09:12 bbuchfink

Hi,

Thanks for the input, I did consider this. Unfortunately we're using the entire NCBI nr database so we can cover everything. Although I prepared it for use with diamond (prepdb), I don't have (and can't reasonably get) all of the raw sequences to manually make it as a diamond database. As such, I'm not really sure that's an option, unless there's a pre-existing version of the NCBI nr database in diamond format somewhere!

Jan 03 '23 15:01 maggielawton

You can download the nr sequences from NCBI https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/, or extract them from the nr database blastdbcmd -entry all -db nr -out nr.fasta

Jan 03 '23 16:01 DarrenObbard