nr database Diamond

Question

[Dave Th]

Hi guys,

I want to use DIAMOND for my metagenome Functional analysis. As the instruction, I have to download NCBI nr database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Unfortunately, my internet connection is not very stable, so I have to download a multiple nr file nr.**.tar.gz instead of a nr single gz file using these code:

wget 'ftp://ftp.ncbi.nih.gov/blast/db/nr.01.tar.gz';
cat nr.**.tar.gz | tar -zxvi -f - -C

After that, I got a lot of file in my output directory (~180Gb). I wonder how I can combine all these file into a single nr.faa just like in the DIAMOND manual.

Thank you all.

Dave

Answer 1

[h.mon]

DIAMOND needs its own database, it does not work with blast databases - which is what you are downloading. You have to download the NR fasta file, then:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
diamond makedb --in nr.gz -d nr

Edit at 2022/11/08

Since DIAMOND version 2.0.8, DIAMOND can use original BLAST databases. One has to call diamond prepdb before using native BLAST databeses.

[GenoMax]

DIAMOND also needs more RAM than BLAST+. Something to keep in mind.

[O.rka]

How long does it usually take to build nr with diamond using all of the taxonomy files?