Metagenome mode with ALL kingdoms

[tseemann]

I use your tool "Prokka" (version 1.10) with your the default rRNA predictor "Barrnap" mainly for metagenome-annotation (and am very happy with it).

As my metagenomes consist of bacterial as well as archeal components, I already created a custom kingdom BLAST-DB for prokka (based on concatenated bacterial + archeal swissprot databases) for the protein annotations.

Now I would like to do something similar for the RNA prediction step with Barrnap (to increase the sensitivity). Is it possible to create custom HMM-DBs for Barrnap?
Otherwise it seems that the best option for me would be to replace the "bacterial" library with a concatenated archea+bacteria library, (As it is the default and will therefore probably be used when I run prokka with my custom-kingdom setting).

Thank you and with friendly greetings,
John Vollmers

[rohansachdeva]

Just curious if this is still in the works?

Thanks!

[tseemann]

@rohansachdeva haven't had much time. Would you have a link to an assembled metagenome that would have representatives from multiple kingdoms?

[lalalagartija]

Hi,
I am also using Barrnap on my metagenomes and I wondered if the option to add fungi is released or not yet (because they are present in my samples).
Thanks a lot