adding tools for bacterial pathogen detection

[sche2021]

Hello,

I don't know where I can post this request, but I think it would be important to add new tools on the Galaxy.eu for bacterial typing.

1) chewbacca is a tools for core genome MLST typing: https://github.com/B-UMMI/chewBBACA

2) grapetree for creating multispanning tree on cgMLST matrix https://github.com/achtman-lab/GrapeTree

3) confindr tool is useful to find bacterial intra-species contamination in raw Illumina data. It does this by looking for multiple alleles of core, single copy genes: https://github.com/OLC-Bioinformatics/ConFindr

Thank you for considering my request

[bgruening]

:heart: thanks a lot for your input.

We are not sure when we can work on this, but we will put this on our todo list. Thanks for your interest.

[bebatut]

Thank you @sche2021 for your request!

microGalaxy is a community of practice focused on microbial data analysis in Galaxy. We are working on a curated list of tools available in Galaxy but also a tool wishlist. I added the tools you mentioned in the wishlist. Your input as this request is really important to us to identify where we need to put our efforts.

We would love to hear more about your use cases where Galaxy was beneficial, and also the barriers you might have. The aim is to collectively find solutions to improve user experience and reduce barriers. To this end, we launch a short survey (open until April 20th): https://forms.gle/q8LizeoHCxjjQp559

You can find more information about this survey and how we plan to use it on the dedicated post here: https://galaxyproject.org/news/2023-03-21-microbial-survey

Also, if you are interested in participating in the microGalaxy community of practice, you are more than welcome:

• We will have a community meeting next month (likely on April 27th)
• We have a mailing list where I could add you for updates
• We have also a chat where you could ask your questions or submit request

Thank you!