[question] Polishing steps.

[lfenske-93]

Hi Robert,

I wonder if Bactopia involves specific polishing steps? I mean to have seen some things in the complete usage, but no direct listing.

The background is that @oschwengers has built a nextflow-workflow for our workgroup some time ago, which contains some such polishing steps and for this reason we currently like to use it for our internal analyses.
However, we would also like to use Bactopia more, as it simply makes many things much easier. 😄

We are thinking especially of tools like:

• pilon
• polypolish
• masurca
• racon
• medaka

Maybe @oschwengers has even more in mind. 🤔
Does Bactopia already include this and is it possible to switch the steps on and off flexibly?

Looking forward to your reply.
Greetings,
Linda

[rpetit3]

Hi @lfenske-93

Bactopia has the polishing steps that are built into Shovill (bwa, pilon) and Dragonflye (racon and/or medaka, and if having short reads polypolish and/or pilon).

I wanted to get masurca into Dragonflye, but there was a conflict with other packages already in Dragonflye. We could potentially get a few more added into Shovill.

Cheers,
Robert

[oschwengers]

Hi Robert, thanks for the quick reply!

Great to hear that these are already included in Bactopia - I wasn't aware of this. However, since I've recently come across Ryan Wick's work on genome polishing, in particular PolyPolish, I was wondering if we could somehow add additional genome polishers like PolyPolish and (HyPo into Bactopia, either directly or via Shovill. They seem to give good performance due to the PolyPolish paper.

Thanks and cheers!

[rpetit3]

Let me see what I can do about adding Polypolish to Shovill. I think it should be able to pull from Dragonflye and drop it into Shovill (since Dragonflye is more or less a fork of Shovill).

I'll look into adding HyPo into Dragonflye as well