genecad

Run `npx skills add plantcad/genecad --all -g -y` in your terminal to install all skills in this suite globally. Note that running the underlying pipeline itself requires a Linux machine with an NVIDIA CUDA GPU.

GeneCAD predicts gene structures directly from genome FASTA files using the PlantCAD2 DNA foundation model. It produces standard GFF3 annotation files without needing RNA-seq or protein evidence.

Yes, an experimental vertebrate model is available alongside the default plant model. The animal model is still in development, so results should be evaluated carefully before production use.

You need a Linux machine with an NVIDIA GPU with at least 16 GB of VRAM and CUDA 12.4 or newer. An A100 or H100 GPU is recommended for large genomes like wheat or barley.

Use the built-in evaluation command to compare predictions against a reference annotation. It reports CDS recall, splice site motif distributions, and BUSCO completeness scores.