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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Accept Glimmer predictions file instead of running Prodigal #180

Open blawlor opened 8 years ago

blawlor commented 8 years ago

I would like to propose a new feature: to allow Prokka to be called with the output of Glimmer. This would cause the Prodigal step to be skipped. Instead, the Glimmer output file would be parsed according to its own format, and used to build up features in an analogous fashion.

I have a patch that does this already, which I would like to offer in a Pull Request. I'm creating this issue in order to help track that PR.

blawlor commented 8 years ago

Bump.

tseemann commented 7 years ago

I think it would be better if I supported loading a GFF3 file of existing annotations. It is a more general solution to the problem. I'm hesitant to add anything major like this until I finally get v1.12 out.

DeepakKumar1986 commented 5 years ago

Do we have any progress on this matter? I use prokka and would be thrilled to see the ORF predictons coming from GLimmer or Genemark then prodigal. In addition, if prokka could be made to compare the results of these three ORF predictors and out the best predictions for annotations. Thanks!