Alternative tools for orf prediction

[kdm9]

Hello all, thanks for squanti.

We've written an end-to-end isoseq pipeline that uses squanti, and as part of that I'm making a bioconda package for squanti. It seems like it should be reasonably straightforward, with the exception of genmarkS-T. Given the repeated issues with gmst (#224, Magdoll/SQANTI2#26, #199, #104, and many many more), and the fact that AFAICT redistributing GenMarkS-T is forbidden by their licence terms, it seems wise to replace it with an alternative ORF predction algorithm. Is this something you've considered? If not, could I please encourage you to switch gmst out for something like https://github.com/urmi-21/orfipy or even transdecoder?

If this is something you'd be willing to accept, then I can have a quick go at implementing such a change.

best,
K

[carolinamonzo]

Hello @kdm9! Thanks a lot for using SQANTI3! We are very happy you like the tool and are implementing a bioconda package using it!. Apologies for the delayed response.
We have been thinking about orfipy lately. However, no one is currently working it's implementation. If you are interested in implementing it, we will be more than happy to accept your pull request!

Best,
Carolina.