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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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BUSCO for cstmm #42

Closed kfuku52 closed 1 year ago

kfuku52 commented 3 years ago

Typically, more single-copy genes can be detected with BUSCO compared with Orthofinder. It doesn't hold the highest priority, but the BUSCO input for cstmm could be a future improvement.

Hego-CCTB commented 3 years ago

yes, I had a similar thought, as I'm currently preparing my data for BUSCO single-copy identification. This will be needed for the upcoming amalgkit csca as well.

kfuku52 commented 3 years ago

amalgkit needs reference transcriptomes anyway, so BUSCO runs could be included as a part of an amalgkit subcommand. It's difficult to do so with OrthoFinder because its computational time should increase exponentially with the number of species. However, BUSCO scales only linearly with species, so it's doable.

kfuku52 commented 1 year ago

@Hego-CCTB I will take care of it if you don't have time.

Hego-CCTB commented 1 year ago

I think you have a much better idea on how to go about this, please take over!

kfuku52 commented 1 year ago

done