FUGUE (Fungal Universe Genome Unification Engine) is a Python tool that allows you to download genomes, CDS, GFF, and proteomes for more than 2,000 fungal species used in its parent project, ALLEGRO. It draws data from NCBI Datasets, FungiDB, EnsemblFungi, and MycoCosm, and removes duplicate downloads. Additionally, FUGUE can:

1. Create CDS from downloaded GFF files and mark the intron/exon boundaries using GFFRead
2. Utilize DIAMOND to create orthogroups for your genes of interest
3. Create the required input for ALLEGRO

You may find the documentation for FUGUE at its GitHub Wiki.

If you run into any issues or have any suggestions for FUGUE, please report them on our GitHub Issues tracker. It's the fastest way to get support and helps us improve FUGUE for everyone. You may also email the authors at their provided e-mail addresses on the publication directly.

FUGUE has been developed and is maintained by Amirsadra Mohseni, and Stefano Lonardi at the University of California, Riverside.

For programmers, if you open one of the scripts and see hard-coded paths, do not panic (e.g., this line). Following the Wiki instructions, you will set your own paths and these scripts will be updated accordingly.