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FOI-Bioinformatics / flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
GNU General Public License v3.0
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Using flextaxd to modify the taxonomy without genomes #35

Closed mw55309 closed 3 years ago

mw55309 commented 3 years ago

Hello!

I had rather hoped to use flextaxd to modify the NCBI taxonomy without providing it without any genomes - however, if I understand it correctly, this is not possible.

What I would like to do is

1) load the NCBI taxonomy only (no genome data) 2) add some additional species and strains (no genome data) 3) dump out the database in NCBI format

Is this at all possible? Will it ever be possible?

Thanks Mick

davve2 commented 3 years ago

Dear Mick,

It is possible to use flextaxd without genomes. Genome annotations are only nessesary for downstream use of for example the Kraken2-build script. It is suggested to add genomes in the tutorial since the tutorial includes building a kraken2 database later on, but this is optional.

To build a flextaxd database without genomes skip the --genome2taxid parameter on database build.

Best regards, David

mw55309 commented 3 years ago

Sorry, my bad, I thought I had experienced an error, but it was just a warning!

2021-01-28 13:10:16,244 custom_taxonomy_databases [WARNI]  Warning no genomeid2taxid file given!

Thank you!

davve2 commented 3 years ago

No problem,

I think your question is relevant. It is currently not clear in the documenation that the --genomeid2taxid parameter is optional, I will go through the documentation and clarify which parameters that are optional!

Thanks for pointing it out!