Any preconfigured databases?

[jolespin]

I'm looking for a method that can say whether an assembly is prokaryotic or eukaryotic. Was thinking this software might be helpful. Do you have any preconfigured databases that have both prokaryotes and eukaryotes?

[dnbaker]

Hi there!

We don't have any preconfigured databases currently, but that is something we plan to put together for Dashing2 in the near future.

You'd have to download the set of genomes from RefSeq. I have a script which you could use to download them, at which point you could compare your assembly against them.

You could do something like the following:

python3 download_genomes.py all
find ref -name '*fna.gz' > refs.txt
echo $PATH_TO_ASSEMBLY > query.txt
dashing dist -Q query.txt -F refs.txt -k11 -Orefseq.matches -o refseq.sizes -p24

But a pre-built database would be much easier to work with, and you wouldn't need the disk space. I'll let you know when that changes.

Thanks!

Daniel