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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
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Functional annotation? #197

Closed rjsorr closed 2 years ago

rjsorr commented 2 years ago

Hi, I'm wondering as to the possibility of incorporating a functional annotation of reads into ganon, such as that in kraken2?

pirovc commented 2 years ago

I was not aware of this function in the kraken2. Could you explain in more detail what do you mean by that?

rjsorr commented 2 years ago

Hi @pirovc, maybe not directly, but as a protein database can be utelized the option is there. I guess with ganon as well? Check this paper out: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00971-1

pirovc commented 2 years ago

It's indeed a very interesting use case, but unfortunately out of scope of ganon features at the moment. However a taxonomic feature will be implemented soon, allowing the use of custom taxonomies which will probably make the re-purposing easier. Thanks for the suggestion.