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ravel-lab / VALENCIA

VAginaL community state typE Nearest CentroId clAssifier
MIT License
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matching taxonomic names to VALENCIA reference set #2

Closed kviljoen closed 3 years ago

kviljoen commented 3 years ago

Hi there,

Thanks for making this code available. I see there's an entry 'Prevotellaceae_bacterium' in the reference dataset – should this be added to f_Prevotellaceae?

Regards, Katie.

michaelfrance commented 3 years ago

Hi Katie,

There is a slight difference between the "Prevotellaceae_bacterium'" and "f_Prevotellaceae" entries. In the case of "Prevotellaceae_bacterium", the sequence matches a specific 16S sequence which originates from a genome/isolate that had not yet been assigned taxonomy beyond being in the family Prevotellaceae. In the "f_Prevotellaceae" case, these sequences were unable to be assigned to a specific 16S sequence but were classified as generally belonging in Prevotellaceae.

kviljoen commented 3 years ago

Hi Michael,

Thanks for clarifying!