Considering Bakta for genome annotation - requested enhancement

[vascokarla]

Is your feature request related to a problem? Please describe.
PHoeNIx uses Prokka for genome annotation, but it’s no longer actively maintained. We’ve noticed differences in annotations between Prokka and Bakta, and since Prokka isn’t updated anymore, it might not be the best option for current workflows, especially for downstream pangenome analyses.

Describe the solution you’d like
Switch to using Bakta for genome annotation. Bakta is actively maintained and produces annotations that align better with current needs.

Describe alternatives you’ve considered

• Sticking with Prokka: This risks using outdated software with no updates.
• Trying Bakta seems to be the best option right now for accuracy and maintenance.

Additional context
We rely on GFF files for pangenome analysis and have observed notable differences between Prokka and Bakta annotations, which could impact our results. Currently, we run Bakta as an additional step in our pipelines, but the annotation process is time-consuming. Integrating Bakta directly into PHoeNIx would streamline our workflow and improve efficiency.

Thanks to all of the developers! PHoeNIx works great for us!

Best,
Karla

[jvhagey]

Hi, thanks for your interest. We looked into switching to Bakta awhile back and the main issue was the database size required. This can present some issues for users so we didn't move forward with it at the time, but I see they have a light version of the database now.... I think the best solution for now would be to provide a parameter for users to choose to use Bakta instead of PROKKA if they want. We will do some digging to figure out if this will screw with anything else before saying we can make it happen, but I think adding a --bakta parameter or something would be the best option so we don't disrupt what might be the only option for others. Curious as to what differences you were seeing that made you want to request this? Thanks for the nudge to bring this convo up in our group again and move this forward!