Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`)

[LijMeh]

Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`)

[memoriasresiduais]

i have the same problem: i could detected different protein variants in the same roary group, despite using -i 100 -s...

[LijMeh]

Thanks for the comment, glad to see I'm not the only person having this issue. From my preliminary testing it seems like Roary only starts working "correctly" when you go down to a 98% threshold. I'm currently working on a tool that independently validates Roary's results (as I need to use it for a paper but obviously don't fully trust it anymore). I'd be happy to share that once it's complete.

[memoriasresiduais]

I also tried Panaroo and same problem: proteins with >98% pooled in the same family, despite -i 100....
Happy to try your tool for validation!

[LijMeh]

For sure, will share once it's finished (hopefully in the next couple of weeks).

In the meantime, have you created a GitHub issue on the Panaroo page? It looks like they're pretty responsive as the program is still being maintained/developed. (I'll probably run my data through it too, but might take a bit to verify I'm having the issue on my end)

[memoriasresiduais]

Hi LijMeh,
i just tried panacota and it seems to be pooling my gene families properly using a cut-off of 100% aa identity (-i 1) (https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#pangenome-subcommand)
I'll do more checks though to be sure.
feel free to reach me directly, if you wish
good luck,
m
[email protected]

[memoriasresiduais]

Just to add for the records:
on my roary analyses w/ -i 100 -s, roary was not only pooling different protein variants in the same roary group, but also placing identical proteins in different groups...
no idea why this happens.