Tools

Where to go for fungal genome data, annotation, and comparative analysis.

Data portals

• FungiDB — genome, transcriptome, and functional data for fungi and oomycetes, with a query interface built for comparative work. The best first stop for most questions.
• MycoCosm — the JGI fungal genomics portal, and the source of many published fungal assemblies.
• NCBI Datasets — assemblies and annotation as bulk downloads when you need to work offline.

Annotation and gene prediction

• Funannotate — a pipeline for annotating fungal genomes end to end.
• gene prediction parameters — Augustus training parameters for a range of fungal species, kept as an archive.
• BUSCO — assembly and annotation completeness against lineage-specific single-copy orthologs.

Archived

The 2006–2007 Gene_prediction pages document how these parameters were originally trained. They are no longer hosted here; the last Internet Archive snapshot is the surviving copy. Kept for provenance, not updated.

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