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Does Prokka do six-frame genome annotations? The corresponding publication does not mention it.

Seemann, Torsten. 2014. “Prokka: Rapid Prokaryotic Genome Annotation.” Bioinformatics 30 (14): 2068–69.

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Yes, Prokka will consider all six-frames, the gene prediction is actually done with Prodigal, paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/

github: https://github.com/hyattpd/Prodigal

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