Bacterial genome annotation
What tools can I use for the annotation for bacterial genomes (complete and/or draft genomes)?
I liked prokka very much but I have the feeling that the annotation is unreliable. I cross-checked a few entries via blast and it was not very accurate for the genes I looked for.
Any advice? Thank you.
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Are you sure you used prokka properly? You can specify a blast database to make predictions more accurate. I would have suggested prodigal for gene annotation but it's included in prokka
Thank you for the hint. How do I find the specific database for an organism and how can I integrate it in the prokka call?
What organism is it? Prokka is only as good as the databases it uses, so if it’s an unknown organism, you might get dodgy results.