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Feature request: replicon rotation #22
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Hi Dan, Thanks for reaching out! I think this is definitely within the scope of Dragonflye. Maybe as a optional step. I saw they recommend circulator, any other stand-alone tools come to mind for you? I know Trycycler has a step as well but it depends on the previous steps. I can also look into this on my end Robert |
Oh great, I'm glad to hear you're open to the idea. I'm not aware of any other stand-alone tools. I did notice that the circlator repo says it's no longer maintained, and honestly I haven't tried it out. We've had generally good experience with unicycler's plasmid rotation, but for overall quality and completeness of hybrid assemblies we've seen that dragonflye is giving better results. So if dragonflye could do the plasmid rotation step too, it would be the best of both worlds! |
This is the one that I couldn't remember, but found it again: https://github.com/gbouras13/dnaapler This one might do the trick |
Looks great! I wasn't aware of dnaapler. One other feature that unicycler includes is to put the start-gene (repA) on the positive strand. We've also seen some plasmids coming out of our hybrid assemblies that are the reverse-complement of plasmids from other assemblies. I just took a quick look at dnaapler and didn't see if it supports that but I hope that could be included. |
Nor I! Looks like a great addition though. Agree that mirroring the Unicycler-implemented functionality in flye assemblies (preferably using same start IMO) would be great. |
Hi @dfornika, I added support for Cheers, |
Hi @rpetit3 that's great, thanks for implementing that. I'm not sure how quickly I'll be able to set up a test run so please don't let me block you from pushing out a release if you're satisfied with the results you're seeing. |
Thought I'd have a go testing from your dev channel using the new changelog version 1.2.0 (since I gave my two cents here) but this didn't work: When this hits the bactopia assembler, do you think you'll disable unicycler rotation and process both outputs with dnaapler for unified |
Yo! @incoherentian Easiest would be to build a dragonflye env with dnaapler, then download the latest commit from here.
I'll have to think about Unicycler, most likely use dnaapler by default with an option to fall back on Unicyler's method, or the opposite. |
Thanks for the mini-tutorial! Was not aware I could just download and chmod a change like that without confusing conda. Dragonflye actively logs dnaapler progress after polypolish:
& dnaapler summary highlighting relevant useful info
Appears to be working perfectly :) |
Hi all! I finally got around to a proper release, v1.2.0 is now available with this feature: https://github.com/rpetit3/dragonflye/releases/tag/v1.2.0 Going to close this for now, please feel free to reopen! |
Would you be open to adding a replicon rotation feature similar to what unicycler does? There's an existing issue on the flye repo that states that it doesn't directly support rotation, and suggests using circlator for that purpose.
The unicycler paper describes its approach:
...or do you see that as out-of-scope for dragonflye?
Thanks for making such a useful tool. It really simplifies the process of creating high-quality hybrid assemblies.
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