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NCBI Prokaryotic Genome Annotation Pipeline
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Strategy for unknown species #237

Closed aboffin closed 1 year ago

aboffin commented 1 year ago

Hi,

Is there a strategy/way to obtain PGAP annotation for unknown species? For example, there are many instances where the taxonomy is only known at family or order level but not genus level. One way that I am trying to work with such genomes is to use a generic species name, say Pyrococcus furiosus in the submol.yaml file and use --taxcheck --auto-correct-tax options to ask PGAP to correct the genus species as it sees fit. Is this the right way or is there a better/more sensible way?

Thank you for the new release that includes nucleotide gene CDS, I appreciate the update!

azat-badretdin commented 1 year ago

Thank you for your question, Senthil!

use --taxcheck --auto-correct-tax options to ask PGAP to correct the genus species as it sees fit

seems like a good idea to try