bactopia
[feature] Adding module for identifying the prophages in the genome?
Related To
- [ ] Bactopia
- [x] Bactopia Tools
Is this related to a problem? A description of what the problem is. Ex. I'm always converting X to Y, cannot adjust parameter Z [...]
Is this something you would like to see added? A description of the analysis and required tools you would like to see. Ex. New tool does "XYZ", a new Bactopia Tool [...]
Describe the solution you'd like A description of what you would like to happen.
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Dear author,
Could you think about adding a module for identifying the prophages in the genome?
Yours, Tonny
Hi @Tonny-zhou
Do you have anything that you would recommend?
Thanks! Robert
Hi again 😄
I would also love this idea, the only thing I can think of is PHASTER (https://phaster.ca/). However, I'm not sure how well that can be integrated because in my experience, both the web interface and the API are very slow for larger amounts of data.
In any case, there are some scripts that make using the PHASTER API a bit easier, e.g. https://github.com/boulund/phaster_scripts maybe something can be done with that.
But if @Tonny-zhou has any other ideas for tools, I'd love to hear them.
Greetings, Linda
Thanks for the suggestion @lfenske-93 !
Would Phigaro be an option? https://github.com/bobeobibo/phigaro This one is on Bioconda and I think might be more straight forward to get into Bactopia
Also open to other options
Hi Robert,
sorry for answering so late, I was on vacation a few weeks.
Never tried Phigaro before, but it sounds nice and I really would like to give it a try. I think Bactopia could definitely benefit from it. I also absolutely agree that it is significantly easier to implement than PHASTER. If I find time in the next few days, I'll compare the results of both tools.
Greetings, Linda