Building DB of Representative Genomes

[ktmbiome-niaid]

Hi!

I'm interested in creating a database of representative genomes. I tried using the command you provided on your github page:

ganon build --source refseq --organism-group archaea bacteria fungi viral \
            --threads 48 --representative-genomes --db-prefix abfv_rs_rg

Unfortunately during filtering of the assembly_summary.txt file, all genomes get filtered out, and thus no database is made. My sense is some miscommunication with the updater script, but I'm not sure. I am able to make databases using several of the other commands on the page, so it seems to be specific to representatives.

Thank you so much!

[pirovc]

Hi! Indeed this is not working at the moment, but it's not related to ganon or genome_updater (the script used to download sequences from NCBI). It's something on the NCBI side, the current assembly_summary.txt (col. 5) is not anymore listing which genomes are representatives :/ I could not find any information about recent changes, so I guess it's a bug.

That's a bummer since the representative genome sub-set was a great reference set to work with. I hope they fix it soon otherwise I would try to implement some alternative way to obtain this sub-set with ganon.

[ktmbiome-niaid]

I found this article from this September: https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/, suggesting they're now calling them reference genomes instead of representatives, and I do see this terminology in the 5th column as well.

One thing I tried in my testing yesterday, thinking this was a possibility, was to use the -u option to change genome_updater's -c option, but nothing I tried would get read correctly by the script (kept telling me it only expects one argument).

[pirovc]

Thanks for the link, I was not aware of the change. I will update the tools accordingly. For now you could use in ganon build:

--genome-updater "\-c 'reference genome'" to get the old representatives, now called reference genomes.

[ktmbiome-niaid]

Thank you so much! Also, confirming that the genome-updater option works!