New tool Addition: Panaroo

[SaimMomin12]

One of our bachelor students at the University of Freiburg (as a part of his Bachelor Project), is currently working on integrating the Panaroo tool into Galaxy. While a pull request (PR) has not yet been created, we will submit an official PR once the tool is ready for review. Our target is to have the tool available by early January next year.

[wm75]

For reference:

bioconda recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/panaroo/meta.yaml
original publication: https://doi.org/10.1186/s13059-020-02090-4
publication comparing pangenome tools like Roary, Panaroo and PanTa: https://doi.org/10.1186/s13059-024-03362-z

[wm75]

PanTa - https://github.com/amromics/panta - might be another interesting tool by itself since it seems to be even more efficient than Panaroo.

[wm75]

Interesting: there is https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo
Why is this AU-specific?

[mthang]

@wm75 @SaimMomin12 I am a member of Galaxy Australia and wrapped panaroo. This request came from our research community. You can test it on https://usegalaxy.org.au/ if you want. Any feedback is welcome and appreciated.

[wm75]

Thanks @mthang, will definitely give it a try!

[wm75]

btw, there is at least a bioconda package for PanTA now (https://github.com/bioconda/bioconda-recipes/tree/master/recipes/panta)

[lsfr3]

@mthang I am currently trying to use Panaroo (Galaxy Australia) with Prokka outputs generated in the same server, but the Panaroo is not recognizing these outputs as they are .gff3 and apparently the acceptable format is only the version 1 of .gff. Do you know how to overcome this situation? Thank you

[mthang]

@lsfr3 I will need to have a second look at the panaroo documentation before adding gff3 file type to the panaroo. It seems like panaroo treats gff and gff3 differently.