Add OrthoSearch of reference files

[Tonny-zhou]

Dear all,
Thank you for this amazing annotation tool for bacterial genomes! I want to known if you can add an option for orthosearch if we have Genbank or Protein FASTA file(s) that we want to annotate genes from as the first priority.
This option has been supplied in softwares dfast-core as "--references" (https://github.com/nigyta/dfast_core) and prokka as "--proteins".

Thanks and regards,
Tonny_Z

[oschwengers]

Hi @Tonny-zhou , thanks a lot for your kind feedback!
Indeed, I've already thought about this sort of feature and I'll address this in the next minor release (1.2). However, that might take a while.

[oschwengers]

Hi @Tonny-zhou , I've implemented a --proteins option to allow users to provide a trusted set of protein sequences as a single Fasta file.

Sequences therein can be annotated with additional information using 2 formats: short and long as described here: https://github.com/oschwengers/bakta#input-and-output

Could you please try if this is working for you as expected? The homology search is implemented as an alignment using Diamond.

I might also implement an accompanying GenBank/EMBL converter somewhen in the future.

I hope that works for you.
Best regards!

[Tonny-zhou]

Thank you so much!!!