Welcome to Funannotate2’s documentation!
Funannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating fungal, plant, and other eukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.
Key Features
Genome cleaning and preparation
Gene prediction using multiple methods (Augustus, GeneMark-ES, SNAP, GlimmerHMM, etc.)
Automated ab-initio training of gene prediction algorithms
Evidence-based gene prediction using transcript andd protein alignment evidence
Functional annotation using various databases (Pfam, dbCAN, MEROPS, SwissProt, etc.)
BUSCO-based quality assessment
Output in various formats (GFF3, GenBank, FASTA, etc.)
Note this documentation was written entirely by augment code’s Agent, expect some errors.