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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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translation-table code 25 #323

Closed ndombrowski closed 3 days ago

ndombrowski commented 1 week ago

Thanks for the great tool,

I have a question: at the moment Bakta allows to choose between translation tables 4 and 11 and I was just wondering if it would be possible to implement code 25 for Candidate Division SR1 and Gracilibacteria as well?

Thanks a lot for considering! Regards, Nina

oschwengers commented 1 week ago

Hi @ndombrowski , thanks for asking. Bakta uses Pyrodigal and BioPython for all internal translations. Based on a quick look into docs/codes of both, this should in principle be no problem.

Could you provide or point me to a public test genome?

ndombrowski commented 3 days ago

Hi @oschwengers, thanks for the quick reply.

There is no type material as far as I know but Aalborg_AAW-1 should do and is also annotated with translation table 25 in NCBI.

Thanks a lot for checking!

oschwengers commented 3 days ago

Thanks a lot!

I've added support for translation table 25. A quick test based on your test genome was successful.

Now, this is active in the main branch, and will be publicly available in the upcoming v1.10.0 - then, Bakta should be ready to conquer Candidate Division SR1 and the Gracilibacteria ;-)

I'll close this. If there are any issues or questions, please, do not hesitate to re-open it.